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I found this software that allows you to raise the default fan speeds. Seems to help for me. http://homepage.mac.com/holtmann/eidac/software/software.html

Yup, same problem here. I'm not too bothered that my Mac Pro runs hot when in use, but after closing all apps and walking away, the fan will still be coming on and off loudly the next day. The machine is on a wooden floor with plenty of space around it. I also have this curious booting...