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While I don't know where the problem may be, you might be able to work around the problem by segmenting your Flash file and then exporting to video in segments. You can then put the pieces back together in a video editor.
Thanks for the tip but I was trying to avoid having to put the clips into a video editor because that tends to cause it's own problems with sync as well. I actually found my answer via an obscure link to some comment on a forum detailing that .wav files (which I was using) will NOT stay in sync in Flash (regardless of the version) due to the particular way Flash compresses them. I switched all the audio to .aif and bam... instant sync. It sure would be nice if the default sound format Adobe uses in thier own Audition program would be compatible with ther own software! After all, wasn't that what the whole unification of the Creative Suite was about? So that all of their 'suite' would work with each other seamlessly?