Will post if this fixes the problem.
Thank you for the post however.
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I suspect that AE is on some level dealing correctly with the file in the wrong way, if you get what I mean. If you edited the file or used multitrack mode, you may have introduced timecode discontinuities, but since AE is agnostic of persistent timecode for the most part, it may try to align the values so they make sense in its mind and skips sections... I would try to convert the file to a more conventioanl 16bit file in Soundbooth, in the process creating a new, "flat" audio file...
Mylenium, thank you for that advice. I did export through Soundbooth to begin with at 16 bit and I tried exporting in After Effects at 16 and 32 bit. Problem persisted regardless.
Thank you however.
Thank you Todd_Kopriva, that seemed to fix my sound problem, however, a new problem was created.
Before the update, when I exported at 1080p PAL it would export with 1080p quality, but in the resolution I specified (576x720), however, after the update, even when PAL 16:9 (576x720) was specified as the export resolution it would export at the resolution of 1080p, so when I play it back, it literally takes over my screen.
How would I fix this so it kept at 16:9 but with 1080p (PAL) quality?
Thank you for the advice and answers.