Why not just use the LMCE structure? Its only the top folders anyway, then everything else is whatever folder structure you have now. Its really not a big deal, but it instantly fixes the problem you are having - btw I don't know if that is by design or a bug, could be either, I just don't worry about it as I use the LMCE strucuture. Bit annoying tho for ad hoc storage devices like thumb drives, mp3 players, etc which you can't necessarily use the LMCE structure.