You can try to put it to run all the time perhaps, see if that helps?
I don't see how this could be related to you changing your startup programs, it might just be random that the problem started just then.
If the fan still wont run, it is either dead or not getting power for some reason. I don't know how easy/hard it is to swap a laptop fan. A repair shop might be the solution (unless it is more than 3 years old in which case a new one is probably almost as cheap) Of cause if it is so new that the company who sold it still has responsibility you should take it up with them.