What mod were you running, and were downloads enabled?
Did you have a very secure RCON password?
EDIT:
I'm aware of a gamecode bug (memory corruption) when NPCs are around (i.e. SP maps) which will overwrite certain values, generally resulting in bots endlessly coming in. It's possible the clantag also got corrupted.
Are you running JA+?
The bug is fixed in OpenJK gamecode and JA++