James -

Auto is *not* hardware controlled. When set to Auto, thinkpad-acpi is
controlling the fan speed directly. When you set it to disengage, this
means thinkpad-acpi is *disengaged* - which is the fan will run at full
speed. Thinkpad-acpi's "algorithm" does not spin the fan up soon enough
or fast enough. "Auto" means acpi is controlling the fan. At least on my
T61 running the latest kernel and Jaunty. Perhaps you are reading
documentation related to an older version or different kernel.

I have not been able to duplicate the overheating issue in any other
version of Ubuntu, nor in Windows XP SP3.

Auto is the default setting and the one that causes the issue.

With the acpi module disengaged, my fan runs between 4000 and 5000 rpm.
The laptop now idles at 45C. I can drive the cpu temp to the mid 90's by
running cpu stress, but the temp does *not exceed* 95C. The high temp is
only achieved when artificially stressing the cpu using the stress
application.

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Ubuntu 9.04 laptop overheat and shutdown
https://bugs.launchpad.net/bugs/370173
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