I have the same problem here after I transitioned from the P2 controller to the new ford truck built-in controller. It seems the OEM Ford truck controller monitors all the of the truck computers and systems and will not send brake magnet voltages if the forward speed measures at the speedometer is less than 10MPH or so. This only happens when just using the truck brake pedal. I get full brake magnet voltages using the manual slider switch. I like to have the trailer brakes ON at a stop sign if I am on a decine so now I have to reach down and hold the manual slider switch along with pushing on the truck pedal brakes to do this.
Your brake controller may be doing the same sort of thing...
I have always had the situation as others have stated here that even when sending brake voltages to the brake magnets they do not engage until a 1/4 of turn on the wheel is accomplished. Some kind of mechanical thing involved...
Using my boy scout compass near the wheels also tells the story for me whether or not the brake magnets are getting power. The brake magnets on my POPUP emit a tone when voltage is applied. The ones on my fifth wheel do not but you can hear a hum if you listen hard.
The book says each brake magnet should draw around 3AMPS with 12VDC applied.
Roy Ken