This output module throws them off. Any ideas? How can we overcome this? I am importing png's and sound/video direct from an slr as a .mov file.
Nobody can tell you anything without proper system info or other technical details like version of AE, render settings, footage interpretation, comp settings and so on.
If your comp frame rate matches your render frame rate and the audio track in AE is from a standard production format at a standard sample rate I've never had the audio out of sync on any render. Examine your workflow and check all the settings. It's far more likely that you have fouled up something in the workflow than you have found a bug.
Thanks for getting back to me, it seems H.264 does not accept frame rates lower than 23.976, I switched from 20 to 25 and problem solved.