I had a 2001 GMC Sierra and when I added the plug-and-play brake controller it just didn't seem right. I couldn't get it dialed-in for my first trip out. When the sun went down, and my automatic headlights turned-on... the trailer brakes locked-up.
A pin inside the truck was in a different position then the brake controller plug. The plug was listed for a 2003 and newer Sierra but the shop that sold it to me assured me that it was the same for 2001. They were wrong, it physically fit but was not right. Check the wiring with a volt meter inside the GMC plug and with the prodigy plug. Sounds like something isn't right.