Don't use export. IMHO it shouldn't even be an option. Use the render cue by choosing Composition>Make Movie or Composition>Add to Render Cue. Exporting can give you all kinds of weird results. The only thing I ever use Export for is to create a swf (flash) movie.
It would help to know what format you were choosing. Flash??? other??? There are tons of things that can go wrong with a GOP compression scheme that could throw the audio out of sync.
Check the audio sample rate when exporting! Most of these sync issues occur because of unnecessary resampling and AE not being an audio tool, this may be problematic and produce these ill effects.
Actually the Render Queue is the only one that gives me entirely bad results. The Render Queue keeps the synch but takes everything from the wrong position. So all the clips start like 2 seconds-ish earlier than they ought to. Just export through file menu preserves the correct video but messes up the audio. That said, I generally agree Render Queue is the way to go.
Anyway, sorry I should have mentioned the rendering format. As far as I have found it has the same mistake in every format I render to.
Yeah, I tried that unfortunately. I went through a ton of different export attempts all with the same results. Thanks for the thought though.