Well that's a bit weird then. If you used a factory harness and it was working all this time then it should be working unless something shorted. You might want to poke your head under the dash and see if the wires to the controller are still hooked up correctly. My WAG (Wild A-- Guess) is that the brake light switch is still a problem.
Find the wiring diagram for your brake controller and make sure that the wires are getting the correct voltages.
For a Prodigy it's
BLACK wire 12V positive.
RED This is the brake switch wire. It should read 0 until you press the brake pedal.
WHITE wire is ground.
BLUE wire is the brake signal. This is typically the 5-o-clock position if you look into the socket on the back of the truck.
From what you are describing I'm betting you are getting 12 volts from the brake pedal when you are not touching it.
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2001 Suburban 4x4. 6.0L, 4.10 3/4 ton **** 2005 Jayco Jay Flight 27BH **** 1986 Coleman Columbia Popup