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No answer, but it does this to me too.
What resolution and codec are you exporting with?
As a test, if you stretch your movie down 50% (in the render queue), do you still get choppy audio?
Are you sure it's really a problem in the file itself? This could merely be a buffering problem with Quicktime in combination with your audio hardware... You should check the file on another system before making any assumptions that may cost you endless test renderings and nerves.
First rule of AE: Avoid "Export" and use the Render Queue instead.
Like Mylenium suggested, render to a codec you know will play easily, such as QuickTime PhotoJPEG at 95% quality. If it is still choppy, then you've found a bug. If your PhotoJPEG-render plays great, then it is you computer that isn't fast enough to play the file from the harddrive.
- Jonas Hummelstrand
I will try some of the suggestions here and report back. Thanks everyone for your input so far.
OK, tried the suggestion from Jonas on avoiding 'Export' and used the render queue instead and... Viola! Worked like a charm.
I went back and scrutinized the differences between the two and found the problem; the export settings were set to 44.1khz for the audio vs. the 48k for my render queue setting. I changed the audio to 48khz for the export settings, tried it again, and this time the problem was gone.
Thanks again for the tips and ultimate solution.