Starting with "Win-OS-Upgrade-K9.2000-2-5" W2K SP4 is included. These upgrades are intended for all installations of (among others) CallManager and IPCC Express/CRS!
The latest available version is "Win-OS-Upgrade-K9.2000-2-6" and SR1 which should be working okay together with the 3.1.3 of IPCC Express.
See also:
http://www.cisco.com/univercd/cc/td/doc/product/voice/c_callmg/osbios.htm
PS. Don't try to install SP4 (or other MS Hotfixes) seperately from these Win-OS upgrades.