Yup, Ace, it sounds like somehow Balance mod stuff got installed and put in the wrong folder, i.e. tremulous/base. You'll have to go through everything in the base folder (in both the user Tremulous directory and the program Tremulous directory) and weed out any files that match
base/data*.pk3
base/vms*.pk3
Leave only data-1.1.0.pk3 and vms-1.1.0.pk3 (these are the original default files). Delete the base/vm folder(s) entirely for now. Then you'll have to re-download TJW's files.
Is this on a computer at school, or your home computer? If you didn't visit a Balance-mod server, or download and install the Balance mod yourself, someone else has probably been messing around with it.