I'm clocking a partial 'me too' on this one. In a particular project in CS6 (although the project was imported from CS5, which may or may not be relevant - the sequence in question was created in CS6) I have a MultiCam source sequence with 6 video and audio sources plus 3 extra audio tracks, and I am trying to mix down a couple of the audio tracks using automation. Whatever I do with automation, I have failed to get it to record any keyframes (except the odd single one right at the start of the sequence). It works fine in other sequences in the same project, and in a test project I created. But there's something about this sequence that means they simply don't take.
I don't know whether this helps anyone with anything, but there is clearly some sort of an issue lurking somewhere.