This can happen with sources that have been edited (commercial breaks removed from tv rips for example). The reason this happens is as follows:
SVCD, VCD & DVDs contain mpeg program streams. In a mpeg program stream there exists presentation timestamps(PTS). These, as you may expect, are used to keep the audio & video in sync. In the MPEG encoding process (TV card or whatever), audio and video may start at a different PTS or some frames may be lost during the recording. You will not notice this when playing back the recording, as the PTS info present in the MPEG2 PS will mean that video and audio will be presented at the correct time, even with frames missing. Audio and video will still be "in sync", as the player knows exactly, when to present the A/V chunks.
Now in order to do a DVD-VCD we have to seperate the elementary streams from the program stream and interleaving them to a new program stream after resampling the audio.
During demuxing we generate elementary streams, that have no timing information. Now - when you re-mux these streams, a missing or corrupted A/V block will lead to de-synchronization of audio and video.....
This is the issue. Everything will work but there will be sync issues as frames are dropped during encoding to maintain sync after the mpeg structure has been cut.
A simple test is to take a mpeg file that has resulted in sync issues. Using any demuxer (e.g TMPGEnc), split the audio from the video. Now multplex them using any muxer (e.g TMPGEnc) without doing anything else. The resultant mpg will be out of sync....
Therefore, just because a mpeg plays in sync doesn't mean it will be in sync after it has being processed, by ANY application, involving demux.
There is a solution:
Finally a SUREFIRE way to add Multiple VCD'S to DVD-R Without Audio Sync Issues
If you don't want to follow the guide you could try to only reencoded the audio of the old mpg with tmpgenc and mux that with the old video file (elementry stream). This method helped me alot. I takes less time and no loss of quality of the video.
And i noticed the it isn't only with eps that are cut also download files that aren't complete downloaded have the same problem.
Contibutions by yf2001usa
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The above is now superseded by:
Also for those files you find that are out of sync, using the above, try duhmez's method:
Fix Av sync without reencoding!! perfect!