I have a 40 Gb or so music collection (mp3's mostly) I let Tunes do it's thing woth the directory, and now a very strange directory sructure has popped into existance. Very strange goings on. Some directories seem to house only cover art, others are now housing multible albums. I don't like it much when programs start altering my filing system without me knowing about it.

I think I'll switch to VLC or something.

Huh, you know, you might try taking a glance on which option you choose, especially when dealing with so much info, before actually pressing it. I'm surprised iTunes didn't actually screw up the integrity of your files, 40 gigs (with average size of 5mb files) is quite a lot you know.