Try and install lm-sensors 
(https://help.ubuntu.com/community/SensorInstallHowto).
Then find out what temperature your cpu / hard drive is .
Then we can see if its a problem with the fan turning when its not meant . ie 
your cpu  temperature is still low.
Or if is indeed that your cpu is getting very hot.

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fan runs often and long time
https://bugs.launchpad.net/bugs/412287
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