Audio is off sync towards end of exported film

I am having an issue which makes no sense so here goes... I animated a short piece which some lipsync in it. I exported it via the Media Encoder. It works perfectly at the beginning but the last two lines of dialog are off a number of frames which makes no sense. The preview in Flash works fine but when I render it the lines are off whether it's swf, flv, mp4 or any format Flash can spit out. Both CS 6 NAD Flash CC do this yet like I said if you play it in the timeline it's dead on sync.
The frame rate is the same in the file and the exporter so that's not it. I can't figure out why. Any thoughts? It was animated in Flash CS6 and then rendered in Flash CC because Flash CS6's rendering is a bucket of poo at best. Any help would be greatly appreciated.

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?

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