Can you go into BIOS and see if the CPU is over heating?
On my system I can adjust fan speed and what the CPU target temperature is (maybe try lowering it).
Are you using any other OS, I know vista and win7 you can lower the CPU utilization thus lowering the temperature emitted. -There maybe something like this in Ubuntu but I have never need to lower the CPU utilization for that.
It may not solve the problem, but it may make your computer more usable.
BTW thermal paste should help dissipate the heat even if the fan isn't working correctly or fast enough.
Xlphos
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