I have almost the same problem. I am on a Fujitsu Siemens Amilo L1310G.
If the laptop is cold (below 50 C) when I start it, the fan does not
start at all. If it is warm when I start it, the fan runs until the
temperature is below 50 C. The fan then turns off, never to turn on
again (even if the temperatures rise above 50C).

The same issue existed in every version I've tried (I started using
Ubuntu with 8.04), but there was a patch on the laptop testing page
(https://wiki.ubuntu.com/LaptopTestingTeam/FujitsuAmiloL1310G under
"From the start). This patch made the fan run all the time which was no
problem. This patch does, however, not seem to work with GRUB 2. I can
at least not find a way of getting it to work.

What can I do to help you fix this bug?

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CPU cooling fan does not start at all
https://bugs.launchpad.net/bugs/451337
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