I am having this same problem on my new mac pro running mavericks and CC AE. I had the exact setup going on my old mac pro for years… only running mountain lion there. Never a problem like this, and I have routinely used all sorts of different audio source files… wav, arc, mp3, aif, u name it. This is now a semi regular problem which began immediately upon switching to my new work setup. IMO, this is an issue with AE not playing nice w the OS system’s audio routing systems … Given the recent AE update w the notorious / inexcusable bug with the whole audio reverting to 8hz in the render settings…(which took nearly a month to be fixed w the most recent update) I find it pretty easy to believe that this is another code blunder on Adobe’s part.
I find restarting After Effects seems to fix the problem. …or sometimes even adjusting the levels of the audio in the timeline will shake it out of this bug…