I am experiencing the same issue on T61 2.6.28-11-generic #42-Ubuntu SMP
Fri Apr 17 01:58:03 UTC 2009 x86_64 GNU/Linux

If I leave a background application running (boinc client, sbackup) the
laptop overheats and shuts down.

I have the cpus throttled back from 2.5 GHZ to 800MHz. Currently running
sbackup the cpu temp is 85C. If I run the CPU at 2.5GHz the temperature
begins to climb and eventually the laptop shuts down.

I have installed tpfand and have manually set the fan to on - however it
is not running fast enough at under 3000 rpm.

Temp report from lm-sensors.

It is running extremely hot.

May 10 22:18:48 pluto kernel: [ 2657.519280] thinkpad_acpi: unhandled HKEY 
event 0x6022
May 10 22:18:48 pluto kernel: [ 2657.520305] ACPI: Critical trip point
May 10 22:18:49 pluto kernel: [ 2657.520308] Critical temperature reached (101 
C), shutting down.

-- 
Lenovo T61p is running very hot after Jaunty upgrade
https://bugs.launchpad.net/bugs/361123
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