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If you've set the affinity (good boy) then you wouldnt have any "dual core" issues, and such issues are not usually dual core related anyway.
You've mentioned that the graphics card is OC'd, set it to default and watch the temps and see how things are. Also, watch out for visual artifacts, such as what appears to be snow, tons of screen tearing, or texture popping in and out.
Also, run your memory through a test of memtest86. Its the best memory tester out there.
I also assume that you have all the proper drivers and chipset stuff up to date. It could be a hitching problem related to hard drive swapping.
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