the best solution is probably to export to mpeg-4 audio from QT6. You'll get better compression/quality than iTunes, and QT will pad any offsets to keep it in sync. Also, mp3 is known to create sync offset problems (because it must end on a full frame or something), but I've not heard of duration problems before.
If that doesn't work, you can Add Scaled the Video to the Audio (not the other way around!) in QT
if that doesn't work, you can fix the sync of your original iTunes movie with this utility I wrote:
Sync-Hole. It makes sync'ing easy, but if you still want more control (if you end up with a movie sometime with multiple audio tracks that are out of sync or something), look for a program called QTMutator