I really can't find anything to explain why this is happening. All audio files are tucked away in their proper folders. And when I do a sync preview I get inconsistent results like this:
I will try to gather more specifics tomorrow. The only thing I can think of right now is that it has to do with the fact that I originally had MB pointed to a different user folder when I installed on this computer. But I'm 99% sure I've changed that everywhere in settings.
Added: Also, podcasts are syncing to two different directories. I know what the difference is between the one file that is syncing correctly and the others, though. The one in the correct place I had added manually (by drag & drop) earlier tonight, because it had become unlinked.