What does the fan speed show as if you use the 'sensors' command (with the lm-sensors package)? If the machine is hot and the fan speed is very low or zero then, if upgrading the kernel doesn't improve it, it's possible that your fan may be faulty. I believe they can be replaced - I got a replacement for my Macbook 2,1 fan from ifixit.com. They may have a replacement for the newer model.

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