Same problem here with Ubuntu 9.04 on a Thinkpad T60. This is annoying like 
hell, the laptop shuts down randomly while lots of applications, VirtualBox, 
etc. are running. The overheat occurs on heavy CPU load with power management 
set to "ondemand". 
Hardware is OK (no overheat in Windows XP), also fan etc. has been cleaned. The 
trip points are set to 127 C (THM0) and 99 C (THM1). The reason for the random 
shutdowns is that THM1 sometimes goes over 99 C, as shown by the kernel 
logfile, which initiates the shutdown.

The only "solution" I have for now is a combination of:

1. Manually set the fan to full speed on boot (echo "level 7" >
/proc/acpi/ibm/fan). It then spins at between 3700 and 3800 RPM, which
is faster than it goes in automatic mode (then it reaches about 3300
RPM).

2. Permanently throttle down both CPU cores to 1.67 GHz

This is obviously not a very satisfying solution but still more acceptable than 
random shutdowns, which regularly destroy my unsaved work, filesystem, and 
virtual machines. 
The real problem seems to be that Ubuntu does not run the fan at its full 
capacity (some prior posts mentioned fan speeds of >5000 RPM)?

-- 
thinkpad CPU overheat ubuntu hardy 8.04 
https://bugs.launchpad.net/bugs/213818
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