Something just appears to be a little bit messed up. You shouldn't need to delete any databases. I just checked my cPanel on Lotus and I seem to have a mysterious database sitting in there. I have only two databases tied into my account, and the only other thing phpMyAdmin shows is information_schema which has never counted against my usage and is pretty much a part of MySQL if I'm not mistaken.
I'm assuming this is just one of those bugs that Corey might've forced out from the work he did earlier.