do you have the original tune? if so you might want to compare the dbw tables (e.g., pedal position vs throttle opening) to see if they were changed.
if they were, the ecu may be damaged
i was initially going to play with mine because there is a dead spot in the thorttle for the first 10%. but every forum post said NO! to it so i didn't and just ended up pre-loading the gas pedal with a bolt (pre-loading a gas pedal .. safety first, right, lol)
failing that it might be a short in the wiring harness itself - with one of the GMPP wiring harness I got the gas pedal would randomly work for several prsses, then stop until i unhooked the battery. it was something within the harness because when i swapped harnesses (same ecu/tb/pedal) the problem immediately went away.