well if you're running the standalone install (.deb package) it shouldn't be permission issues since SS is running as root.
SS has done some weird display things in the past for me but there is usually an internal logic to it. For instance If i have two folders in the same music folder: "Bob" and "bob" only big B "Bob" shows up. you may be running into one of those sorts of issues. If it's practically feasible try
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cd /mnt/music
mv D D.bak
mkdir D
and see if it shows up
then, if the 'new' D shows up, move files from the old "D" into it in small doses re-indexing each time and see if this new folder it disappears on a particular folder?
Perhaps you have a folder with a weird character that SS doesn't like or an odd path?
Admittedly i'm shooting from the hip on this one, but some good ol' troubleshooting may be useful nonetheless
As an aside may I ask
why you organize like this? why bother with the "D" folder when you can just lump all the album folders into your base music folder and let SS handle the index?[/code]
EDIT:
O I just thought, maybe you can delete the index file? I have no idea if such a file even exists or if it's stored internally but perhaps the Index is off? I doubt thats the case if your search is working correctly but I'm just throwing out anything I can think off