This is a known bug, tracked as
FS#12129, that typically occurs when automatic updates have been enabled. I'd like to fix this bug, but I cannot reproduce it.
If you have any insight into what may be triggering this bug, please post it to this tracker item. Also, if the problem does not go away when you run "Initialize Now", please attach an archive of your
/.rockbox/database*.* files to your tracker posting if possible.
Which version of Rockbox are you running? Did you add any files before the bug occurred?
Once you've backed up your
/.rockbox/database*.* for debugging purposes, try deleting those files and disabling automatic DB update, then running "Initialize Now" again.