I've been using different music players lately, and, depending on their settings, they may try to help you organize your collection in one way or another. That's my first question: which music player do you use, and have you checked the "library" settings on it?
The next thing I've come across recently were problems with filenames--especially those that have slashes in them (not a good idea). I've been using
detox to clean up my file names, as gmusicbrowser (the player I use) was having trouble managing the library folders. After some work getting things cleaned up a bit, a LOT of empty folders were left behind.
Anyway, just a couple ideas that may help figure out the cause. Good luck!
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