skaught, I too experienced this but on my home PC. I now use iTunes organize my music then merely foobar to play it. Things work better that way. I'd have iTunes organize it first then copy that over to the Zune, however...
It sounds like Zune organizes the songs for you upon copy, so if there's a way to disable this try it. Otherwise you will be stuck until you find someone that knows about a Zune (not me).
I just finished organizing my songs and let me tell ya, ummm no more ever ever ever... why you ask? Try embedding artwork from itunes and various places online into 1902 songs, insanity... Now really I bought most of that through iTunes and artwork was there already. But for stuff that wasn't and iTunes couldn't get artwork for (anime cds, etc) I had to scan the covers myself :| and embedd + straighten........
Screw that! I'm done, it was way way to long to do, years.... got enough and am done.