I realize this is a pretty stale post by now, but if you or anyone else is still having the problem, it may be that your Submix output is set to surround. If so, it'll say 1-6 at the bottom of the channel strip in the mixer for that Submix. STP will export it as a 6-channel audio file, which I know iTunes doesn't like.
Change the submix output to stereo (1,2), and it should export in stereo, and play nice with iTunes.
Hope this helps!
Matthew Norwood