Where did most of the music come from? I wonder if, as FB suggested, you were in manual manage mode, and have been dragging and dropping the files from, say, the default download folder for your favorite *ahem* file transfer client, and thus they are still there, but not in the default kind of locations you’ve already checked.
Also, what happens if you go File -> Add To Library -> and then point it at c:\ (the root directory of your hard drive)...this should cause iTunes to go deep diving and look at all subfolders for all media files it can handle, and add them to the library...
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-Scott
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