Hi,
I had the same problem yesterday under SuSE 10.0; it was a problem with Punkbuster indeed (the version shipped with TCE 0.49 is now NOT the latest availble, and servers do update automatically, it seems).
For some reason my ET/TCE wasn't able to auto-update.
Fixed by downloading the update punkbuster utility (for Linux):
http://www.evenbalance.com/index.php?page=pbsetup.php
Put it into a directory, run it and configure it for Enemy Territory (Add a game); then let it download the newest PB files.
It worked for me, hope it helps you as well.
cheers,
ntt