Either something is wrong with the controller, or the components were mis-wired. A photo maybe? Photos of the data plate of the fan and power supply? Instructions for the controller? The photo of the controller bottom indicates simple wiring.
I built a pair of stir plates using that same PWM module and they work great.
I use 1/2 liter, 2 liter and 5 liter flasks with 1" and 2" stir bars and can dial from "dimple" to "tornado" on any of them.
Either a miswire (seems unlikely) or you were unlucky and received a defective module...
I found a nintendo enclosure to be perfect when building my stir plate. I don't have any special components inside. No potentiometer or anything. I just use a 16 volt computer power supply and it spins my 12 volt computer fan sufficiently fast. I like the nintendo cause it has internal parts like a power button and power receptacle that can be soldered to. It looks bad ass as well.
Having trouble with photos on the iPad. Will jump to the laptop shortly.
Checked the voltage out on the PWM board. 12.3v with pot thrown to right. 11.9v with pot thrown to left.
Although it's only 0.4v difference, I thought the voltage out of the PWB should be stable but the pulses of power out change with the throw of the pot.
Is it possible to wire the fan backwards? ie - + to - and vice versa.