MadMatt:
when i do the transistor tends to flick on and off and so does the fan(the fan gets horribly annoying when it does 0.o)
The PWM frequency is high enough that the individual pulses should not be perceptible if it's working correctly, so I wonder whether there's something other than PWM happening here. Is it possible the Arduino is resetting for some reason? You could use trace output on the Serial port to find out.