Setting Affinity?
Alright, so I know that PCSX2 uses max 3 cores. Now what I want to know, is if I go into the task manager and say, set cores 0,1,2 to only run on PCSX2, and then set cores 3 to use only FRAPS, would that cause system instability and possibly a BSOD?

I've already found out that if I do that, there is no lag at all and my cpu doesn't even go above 40% usage. But, I've only tried this on Dark Cloud.

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CPUs are made to do just that so there are no issues with doing that at all
Common applications shouldn't and don't decide the cores to use, so they should not conflict with handpicked affinity choice. Tools that specifically define the core to be used may have a problem with this (for example the Prime95 stability test, even so I'm not sure there is actual problem or how it is dealt with).
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