So this has been happening more and more frequently lately. It started about a week ago. I'm using AE CS5.5 on a WIndows 7 AMD comp. The first time I render out my project it renders without sound. However if I duplicate the render in the queue without changing any settings, it includes the audio just fine. I'm using the same settings I have been for all my projects for the last 3 months. Quicktime h264 max quality. I always make sure that audio output is checked.
Also, sometimes I get a black frame at the end of the video file that isn't in the composition. So sometimes I have sound but an annoying black frame, and sometimes I don't have the black frame but I don't have sound either. I am changing NOTHING between each of these renders.
I have a sneaking suspecion that this may be a hardware issue, but can't be sure.
Could be simple media cache issues. Purge the caches and see if it makes a difference.
Looks like that was it. As long as I Purge my caches right before I render it seems to work fine. Thanks for the help!