Typically, the fan will run for about 30 seconds up to a couple of minutes depending how hot the motor is. Sometimes it seems like much longer than what it actually is. I believe the parameters of when the fan turns on and off can be changed through ECMDroid or Spy.
On my bike, I realized when the fan WASN'T turning on upon shutdown, that I had a problem. I expect my fan to at least run for a couple of minutes if the bike was fully warmed up.