The fan may NOT be a "shaded pole" type motor, which makes it a variable speed.
The Coaltroal will vary the speed depending on feed rate. The motor may not like it and not turn on unless it has enough voltage from the CoalTrol, that is why it works when you just plug it in and not hooked to the CoalTrol.
Try the Manual Override for the Fan Control and put it up to 99% and see if it comes on, then vary it down and see if it slows down or shuts off.
Get the Mfr & model of the fan, someone on here can probably look it up and find out if it can vary or not.
More info on the fan controlpreparing stove for winter