There are some machines that adjust the fan speed depending on the system load. Cold is good!
It would help if you would post your system specs, even though you have Ultimate x64, Minecraft can be hard on a system.
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Have you noticed any other performance anomalies?
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Being on a carpet is not bad per se, but it will collect more dust, and dirt.
If you have had it there longer than 6mos. I would consider pulling the case cover to give it a cleaning.