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I'm converting videos using the -s option for multiple resulutions and I want to include a short intro at the begining of the video. but for some reason it skips the second -i so i'm only getting the intro Opener_4.mp4 witout the video hdvd.mkv.

What I've tried: (* i tried with and witout the map option)

ffmpeg -i Opener_4.mp4 -i hdvd.mkv -map 0:0 -map 0:1  
  -s 1836x1080 -map 0:0 -map 0:1 -vf -vcodec libx264 -acodec aac -strict experimental -movflags faststart hdvd_1080p.mp4 
  -s 1224x720 -map 0:0 -map 0:1 -vf -vcodec libx264 -acodec aac -strict experimental -movflags faststart hdvd_720p.mp4 
  -s 816x480 -map 0:0 -map 0:1 -vf -vcodec libx264 -acodec aac -strict experimental -movflags faststart hdvd_480p.mp4 
  -s 612x360 -map 0:0 -map 0:1 -vf -vcodec libx264 -acodec aac -strict experimental -movflags faststart hdvd_360p.mp4 
  -s 408x240 -map 0:0 -map 0:1 -vf -vcodec libx264 -acodec aac -strict experimental -movflags faststart hdvd_240p.mp4 
  -s 244x144 -map 0:0 -map 0:1 -vcodec libx264 -acodec aac -strict experimental -movflags faststart hdvd_144p.mp4

the log

ffmpeg version 1.2.3 Copyright (c) 2000-2013 the FFmpeg developers
  built on Sep  5 2013 03:04:34 with gcc 4.7 (Debian 4.7.1-2)
  configuration: --enable-gpl --enable-libass --enable-libfaac --enable-libfdk-aac --enable-libmp3lame --enable-libopencore-amrnb --enable-libopencore-amrwb --enable-libspeex --enable-librtmp --enable-libtheora --enable-libvorbis --enable-libvpx --enable-x11grab --enable-libx264 --enable-nonfree --enable-version3
  libavutil      52. 18.100 / 52. 18.100
  libavcodec     54. 92.100 / 54. 92.100
  libavformat    54. 63.104 / 54. 63.104
  libavdevice    54.  3.103 / 54.  3.103
  libavfilter     3. 42.103 /  3. 42.103
  libswscale      2.  2.100 /  2.  2.100
  libswresample   0. 17.102 /  0. 17.102
  libpostproc    52.  2.100 / 52.  2.100
Input #0, mov,mp4,m4a,3gp,3g2,mj2, from 'Opener_4.mp4':
  Metadata:
    major_brand     : mp42
    minor_version   : 0
    compatible_brands: mp42mp41
    creation_time   : 2013-03-03 06:57:29
  Duration: 00:00:13.35, start: 0.000000, bitrate: 6744 kb/s
    Stream #0:0(eng): Video: h264 (High) (avc1 / 0x31637661), yuv420p, 1920x1080 [SAR 1:1 DAR 16:9], 6611 kb/s, 29.97 fps, 29.97 tbr, 30k tbn, 59.94 tbc
    Metadata:
      creation_time   : 2013-03-03 06:57:29
      handler_name    : ?Mainconcept Video Media Handler
    Stream #0:1(eng): Audio: aac (mp4a / 0x6134706D), 48000 Hz, stereo, fltp, 125 kb/s
    Metadata:
      creation_time   : 2013-03-03 06:57:29
      handler_name    : #Mainconcept MP4 Sound Media Handler
Input #1, matroska,webm, from 'hdvd2.mkv':
  Metadata:
    creation_time   : 2007-04-07 03:28:47
  Duration: 00:02:01.90, start: 0.000000, bitrate: 19153 kb/s
    Stream #1:0(eng): Video: vc1 (Advanced) (WVC1 / 0x31435657), yuv420p, 1920x1080 [SAR 1:1 DAR 16:9], 29.97 tbr, 1k tbn, 59.94 tbc (default)
    Metadata:
      title           : 1080p VC-1
    Stream #1:1(eng): Audio: ac3, 48000 Hz, stereo, fltp, 640 kb/s (default)
    Metadata:
      title           : Dolby Digital 2.0 640kbps
    Stream #1:2(eng): Audio: eac3, 48000 Hz, 5.1(side), fltp, 640 kb/s
    Metadata:
      title           : Dolby Digital Plus 5.1 640kbps
[libx264 @ 0x2df64c0] using SAR=160/153
[libx264 @ 0x2df64c0] using cpu capabilities: MMX2 SSE2Fast SSSE3 FastShuffle SSE4.2 AVX
[libx264 @ 0x2df64c0] profile High, level 4.0
[libx264 @ 0x2df64c0] 264 - core 125 - H.264/MPEG-4 AVC codec - Copyleft 2003-2012 - http://www.videolan.org/x264.html - options: cabac=1 ref=3 deblock=1:0:0 analyse=0x3:0x113 me=hex subme=7 psy=1 psy_rd=1.00:0.00 mixed_ref=1 me_range=16 chroma_me=1 trellis=1 8x8dct=1 cqm=0 deadzone=21,11 fast_pskip=1 chroma_qp_offset=-2 threads=48 lookahead_threads=8 sliced_threads=0 nr=0 decimate=1 interlaced=0 bluray_compat=0 constrained_intra=0 bframes=3 b_pyramid=2 b_adapt=1 b_bias=0 direct=1 weightb=1 open_gop=0 weightp=2 keyint=250 keyint_min=25 scenecut=40 intra_refresh=0 rc_lookahead=40 rc=crf mbtree=1 crf=23.0 qcomp=0.60 qpmin=0 qpmax=69 qpstep=4 ip_ratio=1.40 aq=1:1.00
[libx264 @ 0x2d8dd80] using SAR=160/153
[libx264 @ 0x2d8dd80] using cpu capabilities: MMX2 SSE2Fast SSSE3 FastShuffle SSE4.2 AVX
[libx264 @ 0x2d8dd80] profile High, level 3.1
[libx264 @ 0x2d8dd80] 264 - core 125 - H.264/MPEG-4 AVC codec - Copyleft 2003-2012 - http://www.videolan.org/x264.html - options: cabac=1 ref=3 deblock=1:0:0 analyse=0x3:0x113 me=hex subme=7 psy=1 psy_rd=1.00:0.00 mixed_ref=1 me_range=16 chroma_me=1 trellis=1 8x8dct=1 cqm=0 deadzone=21,11 fast_pskip=1 chroma_qp_offset=-2 threads=48 lookahead_threads=8 sliced_threads=0 nr=0 decimate=1 interlaced=0 bluray_compat=0 constrained_intra=0 bframes=3 b_pyramid=2 b_adapt=1 b_bias=0 direct=1 weightb=1 open_gop=0 weightp=2 keyint=250 keyint_min=25 scenecut=40 intra_refresh=0 rc_lookahead=40 rc=crf mbtree=1 crf=23.0 qcomp=0.60 qpmin=0 qpmax=69 qpstep=4 ip_ratio=1.40 aq=1:1.00
[libx264 @ 0x2de9c00] using SAR=160/153
[libx264 @ 0x2de9c00] using cpu capabilities: MMX2 SSE2Fast SSSE3 FastShuffle SSE4.2 AVX
[libx264 @ 0x2de9c00] profile High, level 3.1
[libx264 @ 0x2de9c00] 264 - core 125 - H.264/MPEG-4 AVC codec - Copyleft 2003-2012 - http://www.videolan.org/x264.html - options: cabac=1 ref=3 deblock=1:0:0 analyse=0x3:0x113 me=hex subme=7 psy=1 psy_rd=1.00:0.00 mixed_ref=1 me_range=16 chroma_me=1 trellis=1 8x8dct=1 cqm=0 deadzone=21,11 fast_pskip=1 chroma_qp_offset=-2 threads=48 lookahead_threads=7 sliced_threads=0 nr=0 decimate=1 interlaced=0 bluray_compat=0 constrained_intra=0 bframes=3 b_pyramid=2 b_adapt=1 b_bias=0 direct=1 weightb=1 open_gop=0 weightp=2 keyint=250 keyint_min=25 scenecut=40 intra_refresh=0 rc_lookahead=40 rc=crf mbtree=1 crf=23.0 qcomp=0.60 qpmin=0 qpmax=69 qpstep=4 ip_ratio=1.40 aq=1:1.00
[libx264 @ 0x2dee860] using SAR=160/153
[libx264 @ 0x2dee860] using cpu capabilities: MMX2 SSE2Fast SSSE3 FastShuffle SSE4.2 AVX
[libx264 @ 0x2dee860] profile High, level 3.0
[libx264 @ 0x2dee860] 264 - core 125 - H.264/MPEG-4 AVC codec - Copyleft 2003-2012 - http://www.videolan.org/x264.html - options: cabac=1 ref=3 deblock=1:0:0 analyse=0x3:0x113 me=hex subme=7 psy=1 psy_rd=1.00:0.00 mixed_ref=1 me_range=16 chroma_me=1 trellis=1 8x8dct=1 cqm=0 deadzone=21,11 fast_pskip=1 chroma_qp_offset=-2 threads=48 lookahead_threads=5 sliced_threads=0 nr=0 decimate=1 interlaced=0 bluray_compat=0 constrained_intra=0 bframes=3 b_pyramid=2 b_adapt=1 b_bias=0 direct=1 weightb=1 open_gop=0 weightp=2 keyint=250 keyint_min=25 scenecut=40 intra_refresh=0 rc_lookahead=40 rc=crf mbtree=1 crf=23.0 qcomp=0.60 qpmin=0 qpmax=69 qpstep=4 ip_ratio=1.40 aq=1:1.00
[libx264 @ 0x2df1400] using SAR=160/153
[libx264 @ 0x2df1400] using cpu capabilities: MMX2 SSE2Fast SSSE3 FastShuffle SSE4.2 AVX
[libx264 @ 0x2df1400] profile High, level 1.3
[libx264 @ 0x2df1400] 264 - core 125 - H.264/MPEG-4 AVC codec - Copyleft 2003-2012 - http://www.videolan.org/x264.html - options: cabac=1 ref=3 deblock=1:0:0 analyse=0x3:0x113 me=hex subme=7 psy=1 psy_rd=1.00:0.00 mixed_ref=1 me_range=16 chroma_me=1 trellis=1 8x8dct=1 cqm=0 deadzone=21,11 fast_pskip=1 chroma_qp_offset=-2 threads=48 lookahead_threads=3 sliced_threads=0 nr=0 decimate=1 interlaced=0 bluray_compat=0 constrained_intra=0 bframes=3 b_pyramid=2 b_adapt=1 b_bias=0 direct=1 weightb=1 open_gop=0 weightp=2 keyint=250 keyint_min=25 scenecut=40 intra_refresh=0 rc_lookahead=40 rc=crf mbtree=1 crf=23.0 qcomp=0.60 qpmin=0 qpmax=69 qpstep=4 ip_ratio=1.40 aq=1:1.00
[libx264 @ 0x2dcf1e0] using SAR=64/61
[libx264 @ 0x2dcf1e0] using cpu capabilities: MMX2 SSE2Fast SSSE3 FastShuffle SSE4.2 AVX
[libx264 @ 0x2dcf1e0] profile High, level 1.2
[libx264 @ 0x2dcf1e0] 264 - core 125 - H.264/MPEG-4 AVC codec - Copyleft 2003-2012 - http://www.videolan.org/x264.html - options: cabac=1 ref=3 deblock=1:0:0 analyse=0x3:0x113 me=hex subme=7 psy=1 psy_rd=1.00:0.00 mixed_ref=1 me_range=16 chroma_me=1 trellis=1 8x8dct=1 cqm=0 deadzone=21,11 fast_pskip=1 chroma_qp_offset=-2 threads=48 lookahead_threads=2 sliced_threads=0 nr=0 decimate=1 interlaced=0 bluray_compat=0 constrained_intra=0 bframes=3 b_pyramid=2 b_adapt=1 b_bias=0 direct=1 weightb=1 open_gop=0 weightp=2 keyint=250 keyint_min=25 scenecut=40 intra_refresh=0 rc_lookahead=40 rc=crf mbtree=1 crf=23.0 qcomp=0.60 qpmin=0 qpmax=69 qpstep=4 ip_ratio=1.40 aq=1:1.00
Output #0, mp4, to 'hdvd2.mkv_1080p.mp4':
  Metadata:
    major_brand     : mp42
    minor_version   : 0
    compatible_brands: mp42mp41
    encoder         : Lavf54.63.104
    Stream #0:0(eng): Video: h264 ([33][0][0][0] / 0x0021), yuv420p, 1836x1080 [SAR 160:153 DAR 16:9], q=-1--1, 30k tbn, 29.97 tbc
    Metadata:
      creation_time   : 2013-03-03 06:57:29
      handler_name    : ?Mainconcept Video Media Handler
    Stream #0:1(eng): Audio: aac ([64][0][0][0] / 0x0040), 48000 Hz, stereo, fltp, 128 kb/s
    Metadata:
      creation_time   : 2013-03-03 06:57:29
      handler_name    : #Mainconcept MP4 Sound Media Handler
Output #1, mp4, to 'hdvd2.mkv_720p.mp4':
  Metadata:
    major_brand     : mp42
    minor_version   : 0
    compatible_brands: mp42mp41
    encoder         : Lavf54.63.104
    Stream #1:0(eng): Video: h264 ([33][0][0][0] / 0x0021), yuv420p, 1224x720 [SAR 160:153 DAR 16:9], q=-1--1, 30k tbn, 29.97 tbc
    Metadata:
      creation_time   : 2013-03-03 06:57:29
      handler_name    : ?Mainconcept Video Media Handler
    Stream #1:1(eng): Audio: aac ([64][0][0][0] / 0x0040), 48000 Hz, stereo, fltp, 128 kb/s
    Metadata:
      creation_time   : 2013-03-03 06:57:29
      handler_name    : #Mainconcept MP4 Sound Media Handler
Output #2, mp4, to 'hdvd2.mkv_480p.mp4':
  Metadata:
    major_brand     : mp42
    minor_version   : 0
    compatible_brands: mp42mp41
    encoder         : Lavf54.63.104
    Stream #2:0(eng): Video: h264 ([33][0][0][0] / 0x0021), yuv420p, 816x480 [SAR 160:153 DAR 16:9], q=-1--1, 30k tbn, 29.97 tbc
    Metadata:
      creation_time   : 2013-03-03 06:57:29
      handler_name    : ?Mainconcept Video Media Handler
    Stream #2:1(eng): Audio: aac ([64][0][0][0] / 0x0040), 48000 Hz, stereo, fltp, 128 kb/s
    Metadata:
      creation_time   : 2013-03-03 06:57:29
      handler_name    : #Mainconcept MP4 Sound Media Handler
Output #3, mp4, to 'hdvd2.mkv_360p.mp4':
  Metadata:
    major_brand     : mp42
    minor_version   : 0
    compatible_brands: mp42mp41
    encoder         : Lavf54.63.104
    Stream #3:0(eng): Video: h264 ([33][0][0][0] / 0x0021), yuv420p, 612x360 [SAR 160:153 DAR 16:9], q=-1--1, 30k tbn, 29.97 tbc
    Metadata:
      creation_time   : 2013-03-03 06:57:29
      handler_name    : ?Mainconcept Video Media Handler
    Stream #3:1(eng): Audio: aac ([64][0][0][0] / 0x0040), 48000 Hz, stereo, fltp, 128 kb/s
    Metadata:
      creation_time   : 2013-03-03 06:57:29
      handler_name    : #Mainconcept MP4 Sound Media Handler
Output #4, mp4, to 'hdvd2.mkv_240p.mp4':
  Metadata:
    major_brand     : mp42
    minor_version   : 0
    compatible_brands: mp42mp41
    encoder         : Lavf54.63.104
    Stream #4:0(eng): Video: h264 ([33][0][0][0] / 0x0021), yuv420p, 408x240 [SAR 160:153 DAR 16:9], q=-1--1, 30k tbn, 29.97 tbc
    Metadata:
      creation_time   : 2013-03-03 06:57:29
      handler_name    : ?Mainconcept Video Media Handler
    Stream #4:1(eng): Audio: aac ([64][0][0][0] / 0x0040), 48000 Hz, stereo, fltp, 128 kb/s
    Metadata:
      creation_time   : 2013-03-03 06:57:29
      handler_name    : #Mainconcept MP4 Sound Media Handler
Output #5, mp4, to 'hdvd2.mkv_144p.mp4':
  Metadata:
    major_brand     : mp42
    minor_version   : 0
    compatible_brands: mp42mp41
    encoder         : Lavf54.63.104
    Stream #5:0(eng): Video: h264 ([33][0][0][0] / 0x0021), yuv420p, 244x144 [SAR 64:61 DAR 16:9], q=-1--1, 30k tbn, 29.97 tbc
    Metadata:
      creation_time   : 2013-03-03 06:57:29
      handler_name    : ?Mainconcept Video Media Handler
    Stream #5:1(eng): Audio: aac ([64][0][0][0] / 0x0040), 48000 Hz, stereo, fltp, 128 kb/s
    Metadata:
      creation_time   : 2013-03-03 06:57:29
      handler_name    : #Mainconcept MP4 Sound Media Handler
Stream mapping:
  Stream #0:0 -> #0:0 (h264 -> libx264)
  Stream #0:1 -> #0:1 (aac -> aac)
  Stream #0:0 -> #1:0 (h264 -> libx264)
  Stream #0:1 -> #1:1 (aac -> aac)
  Stream #0:0 -> #2:0 (h264 -> libx264)
  Stream #0:1 -> #2:1 (aac -> aac)
  Stream #0:0 -> #3:0 (h264 -> libx264)
  Stream #0:1 -> #3:1 (aac -> aac)
  Stream #0:0 -> #4:0 (h264 -> libx264)
  Stream #0:1 -> #4:1 (aac -> aac)
  Stream #0:0 -> #5:0 (h264 -> libx264)
  Stream #0:1 -> #5:1 (aac -> aac)
Press [q] to stop, [?] for help
Starting second pass: moving header on top of the file q=29.0 size=    3630kB time=00:00:13.31 bitrate=2233.6kbits/s dup=6 drop=0    
[mp4 @ 0x2d8d4e0] Starting second pass: moving header on top of the file
[mp4 @ 0x2de9360] Starting second pass: moving header on top of the file
[mp4 @ 0x2dedec0] Starting second pass: moving header on top of the file
[mp4 @ 0x2df0ba0] Starting second pass: moving header on top of the file
[mp4 @ 0x2dcea60] Starting second pass: moving header on top of the file
frame=  401 fps= 12 q=-1.0 Lq=-1.0 q=-1.0 q=-1.0 q=-1.0 q=-1.0 size=    4548kB time=00:00:13.35 bitrate=2789.7kbits/s dup=6 drop=0    
video:8523kB audio:1165kB subtitle:0 global headers:0kB muxing overhead -53.057493%
[libx264 @ 0x2df64c0] frame I:3     Avg QP:17.44  size: 42261
[libx264 @ 0x2df64c0] frame P:166   Avg QP:22.23  size: 18663
[libx264 @ 0x2df64c0] frame B:232   Avg QP:25.06  size:  5246
[libx264 @ 0x2df64c0] consecutive B-frames: 16.0% 17.5%  9.7% 56.9%
[libx264 @ 0x2df64c0] mb I  I16..4: 55.8% 38.3%  6.0%
[libx264 @ 0x2df64c0] mb P  I16..4: 13.8% 10.0%  0.5%  P16..4: 40.1%  5.7%  2.9%  0.0%  0.0%    skip:26.9%
[libx264 @ 0x2df64c0] mb B  I16..4:  0.4%  0.2%  0.0%  B16..8: 31.4%  1.7%  0.2%  direct: 1.4%  skip:64.7%  L0:39.9% L1:56.8% BI: 3.3%
[libx264 @ 0x2df64c0] 8x8 transform intra:40.7% inter:82.6%
[libx264 @ 0x2df64c0] coded y,uvDC,uvAC intra: 16.4% 37.0% 3.3% inter: 6.3% 16.0% 0.1%
[libx264 @ 0x2df64c0] i16 v,h,dc,p: 37% 26%  7% 30%
[libx264 @ 0x2df64c0] i8 v,h,dc,ddl,ddr,vr,hd,vl,hu: 26% 21% 34%  3%  4%  4%  3%  3%  3%
[libx264 @ 0x2df64c0] i4 v,h,dc,ddl,ddr,vr,hd,vl,hu: 21% 17% 41%  4%  5%  4%  3%  3%  2%
[libx264 @ 0x2df64c0] i8c dc,h,v,p: 61% 21% 14%  3%
[libx264 @ 0x2df64c0] Weighted P-Frames: Y:31.3% UV:29.5%
[libx264 @ 0x2df64c0] ref P L0: 71.5%  8.9% 15.0%  4.5%  0.0%
[libx264 @ 0x2df64c0] ref B L0: 90.9%  7.7%  1.5%
[libx264 @ 0x2df64c0] ref B L1: 95.8%  4.2%
[libx264 @ 0x2df64c0] kb/s:2655.87
[libx264 @ 0x2d8dd80] frame I:3     Avg QP:17.88  size: 25469
[libx264 @ 0x2d8dd80] frame P:141   Avg QP:22.69  size:  9944
[libx264 @ 0x2d8dd80] frame B:257   Avg QP:25.83  size:  2403
[libx264 @ 0x2d8dd80] consecutive B-frames: 11.5%  8.0%  3.7% 76.8%
[libx264 @ 0x2d8dd80] mb I  I16..4: 48.3% 42.9%  8.8%
[libx264 @ 0x2d8dd80] mb P  I16..4:  8.8%  9.5%  0.6%  P16..4: 42.2%  8.5%  4.2%  0.0%  0.0%    skip:26.1%
[libx264 @ 0x2d8dd80] mb B  I16..4:  0.2%  0.1%  0.0%  B16..8: 30.2%  2.4%  0.4%  direct: 1.8%  skip:64.8%  L0:38.7% L1:55.8% BI: 5.5%
[libx264 @ 0x2d8dd80] 8x8 transform intra:49.2% inter:74.2%
[libx264 @ 0x2d8dd80] coded y,uvDC,uvAC intra: 23.3% 39.3% 4.8% inter: 6.7% 12.8% 0.2%
[libx264 @ 0x2d8dd80] i16 v,h,dc,p: 38% 22%  5% 35%
[libx264 @ 0x2d8dd80] i8 v,h,dc,ddl,ddr,vr,hd,vl,hu: 25% 23% 25%  4%  6%  5%  6%  4%  4%
[libx264 @ 0x2d8dd80] i4 v,h,dc,ddl,ddr,vr,hd,vl,hu: 20% 20% 33%  5%  6%  5%  5%  4%  3%
[libx264 @ 0x2d8dd80] i8c dc,h,v,p: 63% 20% 13%  4%
[libx264 @ 0x2d8dd80] Weighted P-Frames: Y:28.4% UV:27.0%
[libx264 @ 0x2d8dd80] ref P L0: 67.9% 12.2% 14.6%  4.9%  0.4%
[libx264 @ 0x2d8dd80] ref B L0: 94.3%  4.8%  0.9%
[libx264 @ 0x2d8dd80] ref B L1: 98.2%  1.8%
[libx264 @ 0x2d8dd80] kb/s:1253.22
[libx264 @ 0x2de9c00] frame I:3     Avg QP:18.17  size: 15799
[libx264 @ 0x2de9c00] frame P:132   Avg QP:22.99  size:  5465
[libx264 @ 0x2de9c00] frame B:266   Avg QP:26.61  size:  1050
[libx264 @ 0x2de9c00] consecutive B-frames: 10.0%  3.0%  5.2% 81.8%
[libx264 @ 0x2de9c00] mb I  I16..4: 45.1% 43.3% 11.7%
[libx264 @ 0x2de9c00] mb P  I16..4:  6.1%  8.5%  0.5%  P16..4: 42.7% 12.0%  6.5%  0.0%  0.0%    skip:23.8%
[libx264 @ 0x2de9c00] mb B  I16..4:  0.1%  0.1%  0.0%  B16..8: 30.1%  3.0%  0.6%  direct: 2.1%  skip:64.0%  L0:38.0% L1:55.4% BI: 6.6%
[libx264 @ 0x2de9c00] 8x8 transform intra:54.3% inter:64.3%
[libx264 @ 0x2de9c00] coded y,uvDC,uvAC intra: 30.7% 42.3% 6.9% inter: 7.3% 10.8% 0.5%
[libx264 @ 0x2de9c00] i16 v,h,dc,p: 36% 22%  6% 36%
[libx264 @ 0x2de9c00] i8 v,h,dc,ddl,ddr,vr,hd,vl,hu: 22% 21% 24%  4%  6%  6%  7%  4%  5%
[libx264 @ 0x2de9c00] i4 v,h,dc,ddl,ddr,vr,hd,vl,hu: 22% 21% 23%  6%  8%  6%  6%  5%  4%
[libx264 @ 0x2de9c00] i8c dc,h,v,p: 63% 20% 13%  5%
[libx264 @ 0x2de9c00] Weighted P-Frames: Y:25.0% UV:22.7%
[libx264 @ 0x2de9c00] ref P L0: 65.8% 15.4% 13.4%  5.0%  0.4%
[libx264 @ 0x2de9c00] ref B L0: 95.2%  4.1%  0.7%
[libx264 @ 0x2de9c00] ref B L1: 98.3%  1.7%
[libx264 @ 0x2de9c00] kb/s:626.67
[libx264 @ 0x2dee860] frame I:3     Avg QP:18.31  size: 11356
[libx264 @ 0x2dee860] frame P:130   Avg QP:23.11  size:  3716
[libx264 @ 0x2dee860] frame B:268   Avg QP:26.88  size:   592
[libx264 @ 0x2dee860] consecutive B-frames:  9.2%  3.5%  4.5% 82.8%
[libx264 @ 0x2dee860] mb I  I16..4: 42.9% 43.6% 13.5%
[libx264 @ 0x2dee860] mb P  I16..4:  4.5%  8.6%  0.7%  P16..4: 42.2% 15.0%  7.7%  0.0%  0.0%    skip:21.3%
[libx264 @ 0x2dee860] mb B  I16..4:  0.2%  0.2%  0.0%  B16..8: 30.3%  2.7%  0.6%  direct: 2.0%  skip:64.0%  L0:36.6% L1:57.5% BI: 5.9%
[libx264 @ 0x2dee860] 8x8 transform intra:58.8% inter:59.5%
[libx264 @ 0x2dee860] coded y,uvDC,uvAC intra: 35.8% 47.0% 8.6% inter: 7.8% 10.4% 0.8%
[libx264 @ 0x2dee860] i16 v,h,dc,p: 35% 25%  7% 33%
[libx264 @ 0x2dee860] i8 v,h,dc,ddl,ddr,vr,hd,vl,hu: 23% 24% 21%  4%  6%  5%  6%  4%  6%
[libx264 @ 0x2dee860] i4 v,h,dc,ddl,ddr,vr,hd,vl,hu: 20% 30% 18%  5%  7%  6%  6%  4%  4%
[libx264 @ 0x2dee860] i8c dc,h,v,p: 59% 22% 13%  5%
[libx264 @ 0x2dee860] Weighted P-Frames: Y:21.5% UV:18.5%
[libx264 @ 0x2dee860] ref P L0: 64.5% 17.5% 12.8%  5.0%  0.2%
[libx264 @ 0x2dee860] ref B L0: 94.1%  4.9%  1.0%
[libx264 @ 0x2dee860] ref B L1: 98.0%  2.0%
[libx264 @ 0x2dee860] kb/s:404.07
[libx264 @ 0x2df1400] frame I:2     Avg QP:18.75  size:  7873
[libx264 @ 0x2df1400] frame P:143   Avg QP:23.38  size:  1808
[libx264 @ 0x2df1400] frame B:256   Avg QP:27.86  size:   178
[libx264 @ 0x2df1400] consecutive B-frames: 13.5%  3.0%  3.7% 79.8%
[libx264 @ 0x2df1400] mb I  I16..4: 56.9% 23.1% 20.0%
[libx264 @ 0x2df1400] mb P  I16..4:  3.2%  6.0%  0.4%  P16..4: 41.8% 18.2%  9.7%  0.0%  0.0%    skip:20.8%
[libx264 @ 0x2df1400] mb B  I16..4:  0.1%  0.0%  0.0%  B16..8: 30.1%  1.3%  0.3%  direct: 1.0%  skip:67.1%  L0:33.7% L1:63.0% BI: 3.4%
[libx264 @ 0x2df1400] 8x8 transform intra:57.2% inter:54.7%
[libx264 @ 0x2df1400] coded y,uvDC,uvAC intra: 40.7% 48.7% 11.3% inter: 8.7% 10.8% 1.4%
[libx264 @ 0x2df1400] i16 v,h,dc,p: 44% 20%  8% 28%
[libx264 @ 0x2df1400] i8 v,h,dc,ddl,ddr,vr,hd,vl,hu: 15% 26% 20%  5%  7%  6%  8%  5%  7%
[libx264 @ 0x2df1400] i4 v,h,dc,ddl,ddr,vr,hd,vl,hu: 17% 25% 14%  6%  9%  7%  8%  7%  6%
[libx264 @ 0x2df1400] i8c dc,h,v,p: 61% 22% 12%  5%
[libx264 @ 0x2df1400] Weighted P-Frames: Y:19.6% UV:17.5%
[libx264 @ 0x2df1400] ref P L0: 63.5% 21.5% 10.5%  4.4%  0.0%
[libx264 @ 0x2df1400] ref B L0: 95.3%  3.8%  0.8%
[libx264 @ 0x2df1400] ref B L1: 98.0%  2.0%
[libx264 @ 0x2df1400] kb/s:191.33
[libx264 @ 0x2dcf1e0] frame I:3     Avg QP:20.44  size:  3117
[libx264 @ 0x2dcf1e0] frame P:258   Avg QP:23.63  size:   482
[libx264 @ 0x2dcf1e0] frame B:140   Avg QP:28.53  size:    58
[libx264 @ 0x2dcf1e0] consecutive B-frames: 52.1%  3.0%  3.0% 41.9%
[libx264 @ 0x2dcf1e0] mb I  I16..4: 37.5% 47.2% 15.3%
[libx264 @ 0x2dcf1e0] mb P  I16..4:  1.3%  2.8%  0.5%  P16..4: 34.8% 13.6%  7.5%  0.0%  0.0%    skip:39.4%
[libx264 @ 0x2dcf1e0] mb B  I16..4:  0.1%  0.1%  0.0%  B16..8: 23.6%  0.5%  0.1%  direct: 0.3%  skip:75.4%  L0:24.2% L1:73.3% BI: 2.5%
[libx264 @ 0x2dcf1e0] 8x8 transform intra:57.7% inter:58.0%
[libx264 @ 0x2dcf1e0] coded y,uvDC,uvAC intra: 46.2% 56.9% 18.9% inter: 11.2% 13.8% 2.6%
[libx264 @ 0x2dcf1e0] i16 v,h,dc,p: 51% 18% 11% 21%
[libx264 @ 0x2dcf1e0] i8 v,h,dc,ddl,ddr,vr,hd,vl,hu: 12% 28% 21%  5%  7%  5%  9%  5%  9%
[libx264 @ 0x2dcf1e0] i4 v,h,dc,ddl,ddr,vr,hd,vl,hu:  8% 53%  9%  4%  6%  5%  6%  3%  7%
[libx264 @ 0x2dcf1e0] i8c dc,h,v,p: 57% 27% 10%  5%
[libx264 @ 0x2dcf1e0] Weighted P-Frames: Y:10.5% UV:8.9%
[libx264 @ 0x2dcf1e0] ref P L0: 68.0% 21.4%  7.2%  3.4%  0.0%
[libx264 @ 0x2dcf1e0] ref B L0: 90.9%  6.8%  2.3%
[libx264 @ 0x2dcf1e0] ref B L1: 97.6%  2.4%
[libx264 @ 0x2dcf1e0] kb/s:84.71

real    0m35.185s
user    4m51.602s
sys 0m30.390s

Merging won't help me here because the second video is uploaded by the client and can be in many different formats and codecs (avi, mp4, mpeg, mpg, ts, mp4...) my original thought was to convert both of the videos to mp4 and join them, but than I have problem with two MOOV atoms and it's not suitable for streaming How to merge 2 mp4 files with 1 atom?

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Please include the complete console output. –  LordNeckbeard Oct 3 '13 at 20:49
    
@LordNeckbeard edited. –  user2783132 Oct 3 '13 at 21:03
    
Did you check this link? ffmpeg.org/faq.html#How-can-I-concatenate-video-files –  willus Oct 4 '13 at 5:38
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1 Answer

You have to concatenate the intro and main file. Unless i have misunderstood your requirement. You can use demuxer; filter; or protocol methods. See this:

http://ffmpeg.org/trac/ffmpeg/wiki/How%20to%20concatenate%20%28join,%20merge%29%20media%20files

and this:

http://ffmpeg.org/ffmpeg-filters.html#concat

You say that the second video could be in a variety of formats. In that case re-encoding is the only option. Filter seems to work in those scenarios.

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