I’m struggling with a similar problem. I’m trying to export a QT version of a half hour tv show. By the time I’m 3/4 the way through, the audio is out of sync. All my media is 16 bit 48k. In the past I have been successful in trashing ALL the renders, re-rendering the entire timeline and then exporting a QT. For some reason it is not working this time. Very frustrating since I have to spend about an hour to re-render and then output, just to find out its still screwed up.
But try trashing all your render files and re-rendering before output. It might work.
Kenny