Just taking a guess.
Maybe the issue below has some relation to your synch problem:
http://www.womble.com/support/FAQ04.html
Quote:
4.What is video PTS jumps in an MPEG file?
One of your new releases said it has this feature fixed: "Video and audio synchronization problem for MPEG files with video PTS jumps. (BUG)" Can you please explain what does it mean? Will it restamp PTS/DTS when I concatenate few MPEG files together?
In many MPEG hardware and software encoders, the system will drop video frames when it cannot keep up with a real time video input. This could be caused by an insufficient CPU/DSP processor power, temporary memory bandwidth shortage, temporary disk access error, system/disk/memory buffer full, or others. When this occurs, the encoder will introduce a PTS time jump to the presentation time of the next image, while keeping the audio continuous which is less likely to have the same problems as those of the video and which is also more noticeable if a sound drop occurred. Those video PTS jumps are encoded in the packet headers as a multiplexed MPEG stream. Also, the PTS time codes may start at any value in an MPEG file. Thus, each MPEG file will be treated as an independent time code base. When two MPEG files are connected together, the editor will make sure to generate a new continuous PTS time code and preserve all PTS jumps within the original 2 MPEG inputs.
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That is, maybe your author/reencode/mux software does not handle the "PTS jumps" very well. I don't know if there's a fix for this else than trying other software (but I'd like to know if there's one). BTW which softs did you use?