Another possibility for your corrupt files is that you had run another "admin mod" that could have caused conflict.
You should try and delete these files (games.log, jk2mpconfig.cfg, server.cfg) everywhere you find them, and restart the mod.
I have tried repeatedly to recreate the problems you had and was unsuccessful
I therefore conclude that they're not bugs. If nothing else, please make sure you installed the mod right and ran it correctly.