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I join 3 video files using avconv and create a intermediate file, using following syntax

cat inter1.mpg inter2.mpg inter3.mpg > interAll.mpg

inter1.mpg,inter2.mpg contains no audio track.

After create a interAll.mpg I convert it to a mov file using following syntax

avconv -i interAll.mpg 

My problem is, the audio track of inter3.mpg overlaying with video track of innter2.mpg in

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How exactly is it "overlaying"? Does the audio track start too early? Is it distorted? Can you provide a sample video? Does this happen with all videos or just the ones you have? Finally, could you please post the full, uncut console output from avconv? – slhck Dec 10 '12 at 15:03
Ya audio track start it early... No its not destroyed. This happen with all video. – Elby Dec 11 '12 at 5:32

FFmpeg now has the capability to concatenate files internally, you might have better luck with that. It works as follows:

ffmpeg -i "concat:inter1.mpeg\|inter2.mpeg\|inter3.mpeg" -c copy interALL.mpeg

If that doesn't work, you may need to remux them to mpeg transport stream files first:

for f in inter*.mpeg; do ffmpeg -i "$f" -c copy -f mpegts "${f/%mpeg/ts}"; done
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he asked about avconv, not ffmpeg (which is obsolete btw) – BЈовић Feb 24 '13 at 9:31
@BЈовић FFmpeg is not obsolete. Don't trust the misleading message in the Ubuntu packages, which has already been reworded accordingly. FFmpeg is continually being developed (just see their homepage), and in fact, many features in Libav are just ported from FFmpeg, and vice-versa. For more info, see: Who can tell me the difference and relation between ffmpeg, libav, and avconv. – slhck Feb 24 '13 at 9:37

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