Sorry. This got long.
If you can lock all four wheels empty then the brake controller, wiring, and electric brakes are operational. A good thing. The brake controller works by providing a higher voltage to the brake magnets during heavy braking. Yes, the boost on the Prodigy determines the minimum/starting voltage. The contoller works on inertia so standing on the vehicle brakes will cause the electric brake controller to apply more voltage than when you just touch the vehicle brakes.
The factory wiring and length is the issue IMHO. I estimate that you could be losing 25% of your trailer braking power. Without getting too electical...
Each brake likely draws 5 amps at full braking so that is 20 amps on the brake wire/ground on a dual axle trailer. The higher the current (amps), the greater the voltage loss in the wiring and the lower the voltage getting to the brakes. Not good! The problem is that the length of the wire from the battery, through the controller, to the trailer axles is maybe 35feet+ on a big truck and long trailer.
If you have a multimeter you can do a test to confirm the issue. With the truck running and trailer connected, have someone fully squeeze the controller manual trigger as you measure the voltage at various spots. You may find 16 volts at the battery, 14v at the hitch connector and 12v at the electric brakes. 25% loss!
I estimate that icreasing the gage of the wiring to 8AWG (on both the positive and ground) will reduce your loss to 5% . That may not be practical so 10gage =8% loss. Not bad.
Run heavy wire directly from the battery post, through a auto resetting 30amp relay to the the controller input. Run extension cord type wiring from the brake controller back to the 7 pin connector. Two 12ga wires twisted together = one 9 gage wire. For the ground use the frame as you ground "wire" except at the hitch connector. For that run a short 8gage from the 7pin connector to you truck frame and the same on the trailer side - Big bolts, sanded frame and then paint over. Take the ground wires from your electric brakes to good frame grounds close to the axles.
That should make a huge difference.