What are you trying to export? If it's a "muxed" video (multiplexed, I think) then the audio and video are part of the same "stream," which would cause this situation.
Of course, this is all just coming off the top of my head -- I think I've heard about this, and I know multiplexing has something to do with the audio and video streams (stream meaning data -- different from "streaming video") and I've heard of people talking about their video not including audio from these kinds of "muxed" videos.