I had troubles with the audio creeping by the end of my 40 minute movie. By the end, the audio was 3 seconds longer than the video, making it look like a kung-fu movie.

This was because I was following a how-to guide in MacAddict which suggested you export your sound seperate from your QT movie (from iMovie).

First off, make sure you have iMovie 3.0.3 and QT 6.3, otherwise you'll end up with the problem anyway. Next, don't bother exporting your sound seperate as an AIF in long movies. It will sample at a different framerate as the video and you'll end up with longer audio than your movie.

I tried but couldn't get MissingMPEGTools to make me a good MP2 file from my Quicktime movie (dropping the whole idea of using the AIF file altogether). (Maybe someone has a suggestion there... I kept ending up with a 0KB file anytime I tried to run the .mov file through the audio extractor) So I used ffmpegx to pull the audio and video. I muxed them using MissingMPEGTools. That was the trick - using ffmpegx to pull the MP2 and the M1V files. When they muxed, they worked great, and the audio held through all 40 minutes flawlessly.

Again, if anyone knows why I couldn't pull audio from a QT movie in MissingMPEGTools, I'd like to know.