I recently upgraded to Studio '13. I published a presentation for the course owners to review - no problem. When I went to republish after changes, the audio was missing. I reimported the audio and republished. Then when I went to make additional changes, when I previewed the slide, there was no audio. I opened Audio Editor and I did have audio files embedded. I published the course again - audio is missing again!
I've checked the support FAQs about missing audio. None of them apply to this situation. As a side note, I have a different presentation in the same location (on my hard drive) and I just noticed that the PPTA for THAT file is now at 3KB, which I know means the audio is missing from that as well.