This happened to me with CS6 today, and Dave’s tip fixed the prob for me.
I had tried rendering to different formats, & I also tried restarting AE, too. The resulting video files seemed to have audio (and in Quicktime, the little audio meters were even jumping), but I turned up the volume all the way. I still heard no sound.
Once I found this tip, I converted my voice track from MP3 (which I had originally exported straight from GarageBand) to AIFF (again using GarageBand). Then I re-rendered in After Effects CS6.
Now, when I export to the format of my choice, audio is there.
Thanks to Dave! Since there was no error message, and it was supposed to work, I’d never have known what wasn’t working unless I found a tip like Dave’s, and a forum like this one.