I don't know if this is applicable or not. and mostlikely im wrong, but..
i once had a Graphics card that i tweaked with Afterburner.
However when the Afterburner application stopped or was not running in the background the fan speed dropped to 0 , it turned off.
I had to completely remove Afterburner ( registry remarks and all) and do a complete driver wipe in safe mode. And then reinstall the drives in order to get the fan to turn back on.
It might be possible that a driver or overclocker software is not working correctly.
Alternatively, it used to be one could connect the fan ( on some cards) to the motherboad and use the MB bios to control the fan speed but thats not efficient or accurate and im not sure that can be done anymore.