I've seen this happen with CDs that include extra media, I recommend using another app to rip your CDs, like Exact Audio Copy or foobar2000, both provide secure, offset-corrected ripping, freedb database access, and encoding to the format of your choice (MP3, FLAC, Vorbis, etc), though you'll need to download the encoders separately. EAC shows you the extra media as extra, non-rippable info, and foobar2000 simply ignores the extra media when ripping.
Here are some links:
Exact Audio Copy at the Hydrogenaudio wiki
Ripping with foobar2000
CD drive offsets
LAME MP3 encoder at Rarewares
Note that these apps are complicated at first, but they're the best tools for the job.