For no apparent reason After Effects CS6 (220.127.116.11) will no longer output audio to a Quicktime unless I explicitly go into the Output Module and uncheck and then recheck the Audio Output box.
I have a bunch of Output Modules set up with various codecs, all with the default audio enabled. If I set up a render, select one of those Output Modules, and render, the resulting Quicktime will not have any audio encoded. No audio track is created at all, just video (no little VU bars in the lower right corner of Quicktime Player Pro.)
I'm on a Mac Pro running OS 10.7.4, Quicktime 7.6.6.