no no, the thing I said on Linux was only an hypothesis since I wasn't aware of that thing about Punkbuster.
About tracking the servers through their OS, all depends by the game.
For example Half-life shows if it's a windows or linux server in the query's reply, CoD4 (and many other games) no.
Anyway I think that the Linux version is no longer supported by months, the latest available in fact is dated 30 Jan 2008 and is version 1.5:
http://0day.icculus.org/cod/
considering this "update" problem I think the majority of admins run the cod4 server on linux through wine... it's the only idea about I can thing.