oh, i've just thought of something-- this happens in rare instances, but on some DVDs the studio logo that plays before the movie does not contain any audio at all. when you encode such a movie with the studio logo included, it can throw the audio out of sync because the encoding program begins the audio during the part that should have no sound.
if this is the case, you'll have to demux the audio (save it as a separate file), figure out how far out of sync it is, then trim that much off from the beginning of the video. don't be surprised if the part that you trim out ends up containing precisely the part where the studio logo is displayed. then mux the audio & video again, and they should be in sync.
this may not apply to your problem at all, but i have dealt with a few dvds which required this solution.
