I just had this same issue. I was working on a slideshow and decided to render it and look at the progress. I had various songs etc. The first time i rendered it it had all of the audio, however the next time I rendered it, a short 10 second audio clip in the slideshow didn't get into the rendered version. I also need an answer on this one.
I am actually using Movie Studio+DVD, I think version 4 (the newest one). My settings are the basic default ones, haven't changed anything. It is weird that is worked on the first go around, but not on the second and it clearly plays back on the timeline, just not after it was rendered.
I was considering copying the whole timeline to a new project and seeing if that would do it?????
This was a common problem I had with MS, but when I upgraded to VMS, and downloaded the update, the problem appears to be gone. When I upgraded, I called up Sony to buy the 4.0 disk, and the woman there said the downloaded upgrade (to 4.0a) corrected this known problem