Chewtobacca said:

Thanks for the info, HardwareHank. I'll look into mkvmerge. I hope it's as simple as offsetting one track with respect to another. :-)

From here:

$ mkvmerge -o goodsync.mkv -A source.avi -y 12345:200 outofsync.ogg

This would add 200ms of silence at the beginning of the audio track with the ID 12345 taken from outofsync.ogg.

Some movies start synced correctly but slowly drift out of sync. For these kind of movies you can specify a delay factor that is applied to all timestamps - no data is added or removed. So if you make that factor too big or too small you’ll get bad results. An example is that an episode I transcoded was 0.2 seconds out of sync at the end of the movie which was 77340 frames long. At 29.97fps 0.2 seconds correspond to approx. 6 frames. So I did

$ mkvmerge -o goodsync.mkv -y 23456:0,77346/77340 outofsync.mkv