I know you said that you've set your affinity but maybe you should try something else to make absolutely sure it's not the problem, since the issue you're describing is pretty much exactly what happens with the dual/quad core processor issues. To completely eliminate this variable from being the problem you should run an msconfig, and on the second tab you can set how many processors you want your OS to use. Set that to 1, reboot, try again and see if it's still happening.
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