Any clues as to why?
Cyclic use of the same routines for encoding and decoding at the same time, when those routines are not properly made "safe" in terms of memory management. Or something up with the audio. The smart thing to do as a start would be to convert the AC3 file to a conventional WAV, then try that again.
File was an AIFF 48000 24-bit stereo, I converted it because AE doesn't allow ac3 to be imported (AE CS4 BTW...)
I had done this but in my mind it was still an ac3 not an aiff; so I'll try with a WAV.
What are your composition settings?
HDTV 1080 29.97
1920x1080 square pixel
Are you exporting through the Render Queue or are you using the File > Export command?