It depends on what format your music is in, but you could try a normal search using vista's search, with the search criteria being *.mp3 (star dot mp3).
This will pull up every instance of files ending in .mp3, enabling you to copy them to another folder.
EDIT: Then, once you have them all where you want them, use Duplucate Cleaner (click this text) to delete the duplicate files and save your disk space. (End Edit)
As to exactly why this is happening, i have no idea. i dont use Itunes. Sorry
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