Exporting a movie in QT Pro truncates film

I have a 2 minute QT film that is 264/16 bit 48k audio. I want to export it as a 264/Apple lossless audio to get the file size down. When I export it, the audio plays all 2 minutes fine, but the video only goes for 15 seconds and then freezes the rest of the time while the audio plays properly.
Any idea why this is happening? If I export it as a DV movie everything is fine...
Thanks.

Audio does fine, but the video goes for a few seconds and then freezes on a frame and that is as far as it goes video-wise (that frame lasts for over a minute and a half even if I fast forward the video) while the audio plays the complete 2 minute track.

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