Your audio issues have nothing to do with Keylight. You are making a mess of framerates or choosing a bad audio CoDec. Check
And if you can, avoid working with audio in AE all together, at least for final output. Even the dumbest free video encoders can do this better.
Thanks for the quick reply!!
What i'm trying to do is a virtual presenter for a website - So a transparent flash video that automatically plays when you open up a website, and has a person talking.
This my first time ever editing videos - So i'm very new!!
So i'm very new!!
Therefore read this. to the matter at hand I can't really say much. The only real question would be, whether your audio actually is mono. As I said, AE is crap at audio processing and if you expect it to convert a stereo file perfectly, you are placing too much hope. Realyl do consider manipulating your audio elsewhere and then merging it with the rendered video from AE. As a minor, consider encoding the final output in Adobe Media Encoder or similar tools...