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Well I over clocked it up to 4.5, which is a stable frequency for this chip, and it runs fine now with very little frame rate issues. One thing I did notice however is that only one of my cores seems to be being used more then the others. I know the emulator only used 2 cores, but it only seems to be using one.
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Windows is spreading the load to all 4 cores, so you'll never see 2 cores actually pushed to high usage.
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I was reading in the FAQ, and it said there that PCSX2 will only use 2 cores, but windows overrides it and divides the load that wound have been used by 2 over 4?