Hi,
Not sure if you ever found something to set the affinity.
I have seen this apps that's suposed to set affinity for a program, tho I have never used it.
http://www.adsciengineering.com/StartAffinity/
At the time, we had an application that wouldn't run on a core 2 duo cpu, but we ended up buying a new software instead so I never got to try it out.
Grypht