I’m having the same problems as OP. I’m almost certain that its not a program interfering with the fan, because for the past month the fan has been making wheezing grinding noises like its about to go out. Then the noise stopped and I thought the problem went away, but my laptop started heating up quick.
I took it apart and ran it with the lid open, turns out the fan wasn’t working. I started cleaning the mainboard and the cpu fan thinking that maybe some dust bunnies had jammed it up, turned it back on and still nothing. I’m thinking of replacing the fan but haven’t figured out a way to remove it (2 big brass screws are holding it place)
The part number that I got off the fan Toshiba DC Brushless, MCF-513AM05-1, DC5v 250mmA
Right now Im using a laptop cooling pad and staying away from anything that would tax the cpu too much (afraid of overheating)
So any help anyone can provide would be appreciated, any diagrams how to’s or pics on replacing the fan 
Thanks