Well... My problem went away just as mysteriously as it appeared. After my computer had a good night's rest I tried rendering the comp again with lossless animation and I got mixed audio just as I had originally expected.
I suspect the problem may be a memory problem somewhere. I am getting errors from After Effects saying that it does not have sufficient memory to do something occasionally. Purging things seems to cure the immediate problem, but I suspect I there may be a memory leak somewhere. The composition consists of still photos and animated text layers with a lot of animated masks.
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When rendering, did you have any other audio applications running, e.g. iTunes, a web radio and so on? These may effectively have interfered with AE since as of CS3 it more directly hooks into your audio hardware to accelerate playback and mixing by means of DirectSound/ quicktime, respectively, instead of just software. While working this may not have been noticable, but when you were rendering and may have had another of those programs in the foreground, audio device priorities may have been adjusted and/or your audio driver enabled some specific modes that resulted in incorrect background audio processing...
Thanks. I'm pretty sure I didn't have any other audio application running in the foreground. I may have had iTunes or Soundtrack Pro open but idle. I'll keep this in mind and check other applications if I run into the problem again.