Problem:

After the recent update of the Counter-Strike server protocol to version 48, all the servers I was looking after began to behave quite erratically. The perceived latency boosted to some 200 milliseconds over the normal rate, but all the other server stats (CPU, memory usage) remained quite consistent.

Solution:

After a bit of testing I pinned down the issue to be the new HLDS Linux binary and glibc 2.3.2 incompatibility, which was causing major FPS drops (even below 10) perceived as high latency. More info about this issue can be found in my postings on the VALVe hlds_linux list. Till the moment the bug gets fixed, the way to go is to upgrade the GNU C Library, what can be not that easy if you’re without root access, as was in my case. But nothing is impossible.