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Well, one of them is running a hot processor, a hot Hard disk, and hot memory. The other one is running a relatively cool processor, cool hard disk, and cool memory.
I suggest adding an intake fan to blow over your disk, and at least one more exhaust fan. Also, check to make sure that there's proper airflow through the system.
A final note, Arctic silver blew up my last processor because I didn't know how to apply it properly. You want an extremely thin layer on the chip, because the thermal qualities of Arctic silver is kind of like wool in the summer. The thinner it is the less you sweat.
Good luck, and remember to help your systems breathe.
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I'm married now, so the only thing in my house that pulls out now is the couch. 
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