When a new client and / or server patch is released make sure they're running the latest version of PunkBuster. Steam and HLDS replaces the PB DLL files if they don't match but they can be outdated which least to clients and servers running older versions of PB. They rename the PB files they replace with a "Copy of " prefix.
Latest PB version info can be found at http://www.evenbalance.com/index.php?page=support-hos.php
Issuing the pb_sv_ver command for servers should show this in the server and pb logs.
PunkBuster Server: PunkBuster Server for HOS (v1.837 | A1372 C2.278) Enabled