I’m seeing similar issues with h.264 to ipod but just on selected source DVDs. Only a few seem to generate this bug, and a look in Quicktime Pro confirmed that the audio track on these is shorter than the video track. If a title is out of sync, changing to a different audio track (like commentary) won’t change it.
Hare are a few DVDs and titles that have given me this problem:
Casanova (main feature only)
Zathura (main Feature)
The Sentinel (16x9 group of deleted scenes - doesn’t happen with the 4x3 group and the main feature is fine)
An Unfinished life (main feature only)
Requiem for a Dream (not director’s cut version of this DVD - main feature)
It’s clearly a DVDfab bug since the titles play in other DVD players just fine and the audo sync happens regardless of what I use for playback. But while it’s impossible to predict if a title’s going to have a problem, it doesn’t seem to matter what h.264 settings I use–anything derived from that title is out of sync.