Ok I went to this post
http://www.vistax64.com/tutorials/153125-boot-advanced-options-number-processors.html
When I did this after reboot, started a mission I no longer have to exit out and force the affinity. I now have both cpu's running all the time.
I do not know if this will be a program that hates 2 cpu's at the same time but gonna try this.
Basically go to msconfig and tell sytem to boot two cpu's not one.
Edit I have a e6600 so I changed the cpu boot to two not one. This is for Vista 64 bit.