Hmm sounds like you disabled punkbuster completely. Enter the following in the q3 console: /pb_cl_enable that should enable pb again.

Or maybe you have an older version of pb. Although normally you would get a different kind of error message if that's the case.
Anyway, you can do the following to update pb: go to your Quake3 folder, look for a folder named 'pb'. Inside that folder there should be a program called 'pbweb.exe', run it and wait until it's done.