First off, no, this is a stock phpbb installation.
I'm not quite sure why, but that's where mySQL is storing it's data. It hasn't caused any problems, so I've just left it alone. I have a person I'm hosting running Ikonboard with mySQL as well, he hasn't run into a problem yet.
When I try that query manually, here's what I get:
ERROR 1: Can't create/write to file '/root/tmp/#sql5f3_11d_0.MYI' (Errorcode: 13)