A standard computer fan has its own motor controller built in and can only sensibly be speed controlled
by the speed control input (if it has one), or by setting the analog supply voltage (within limits).
Trying to PWM the entire motor controller will be pushing lots of big current pulses into its decoupling
capacitors - the behaviour will depend on the design of the fan control board.
You can use slow PWM perhaps, 1 Hz or so, to power the fan up and down on a shorter timescale than
it takes to spool down.