As far as I'm aware, you don't need to go through all that hassle with this fix. It automatically does it for you, or at least in my case it does. Alt tabbing out of the game and checking my little cpu gauge tells me that all four cores are actively processing (more than idle tasks).
Here's the description: "This file executes STALKER - Clear Sky, waits for 30 seconds and then sets the affinity to all four cores."
See, automatic. It doesn't tell you to do it. >.
As stated above and in the comments in the link...
"OK, tried it (E4400 dual firstname.lastname@example.orgGHz, WinXP SP3, STALKER CS 22.214.171.124 english, standard CD version) and it works without problems"
Just put the "Affinity.exe" in your Stalker clear sky folder and run it. It should start the game for you and after 30 seconds automatically try and use all of your CPU's cores.
Doesn't the NHancer utility do this as well. And if so, will it have any counter effects if running in conjunction w/ each other? I'm running a Q6600 O/C'd to 3.0 GHz on a Striker Extreme M/B.