EvenBalance.com has a few utilities that will update your version of PunkBuster, and this seems to fix the majority of the problems, however, I've been informed that there are other steps that may be involved.
I have the PB Update tool on my FTP site;
ftp://66.166.156.106/pbweb.exe
Save that to your \ET\PB folder and double-click it. A command prompt will open and start updating things.
The other thing involved is apparently your CD key is validated by PunkBusters servers, and they're apparently swamped with requests. Trying to reconnect several times (and having the most patience in the world) eventually allows you to play (but good luck on crowded servers).
The third thing, is you can
try to manually update your CD key via the console, but this can take a few minutes.
1) Press the Tilde " ~ " key to open the console.
2) At the prompt type:
\pb_sv_enable (press the Enter key)
\pb_cl_enable (press the Enter key)
\pb_sv_update (press the Enter key)
We had PB running on our server, but ended up disabling it because (as usual) it causes more problem than it solves.