In addition to what Rick said, it might be worth to open the file in Soundbooth and convert the sample rate and bit depth of the source fiel as well as flattening the audio tracks. What you describe sounds very much like 24bit audio which AE can't handle properly...
Why bother rendering audio AT ALL?
I work at the ABC affiliate in my town, and when I render out of AE, I never render out the audio. I only use audio for reference. As long as you know what you're doing when you edit and export the green screen shots from your NLE, you shouldn't have any problems.
If you want to make double-dog sure you get the lip-sync right, give yourself 10-frame (29.97) or 20-frame (59.94) handles on the shot at the head and tail. Then if the sync is off -- but it shouldn't be -- it's a simple matter to slide the rendered video file one way or the other in your NLE.