I am flying the free DC-3 that came from Microsoft in the 40th year update and am using the Duckworth mod. I have Cowl Flap Increase and Cowl Flap Decrease functions assigned to one of the 3-way toggle switches on my CH Products Throttle Quadrant, as I have on all aircraft I fly. I have discovered that in order to use that switch, the actual controls for the cowl flaps in the cockpit on the right wall, must be set to OFF for that switch to work. I assume this would be the same for whatever hardware switch you might be using. Not sure if this has been posted before but thought it might be useful to know. 

Yes - I have to set mine to OFF as well (using X-56 with Axis and Ohs).