Don't know if this will help, but we had a similar problem and the answer turned out to be that you need to flatten the movie after adding the audio.
Basically, we had to write the movie to a tmp file, then export that with [QTMovie writeToFile:withAttributes:error]
with an attribute of QTMovieFlatten set to YES.
Hope this helps, so I can start to pay back some of the great tips/answers I've gotten here.