I had the same issue with a 2009 2500 LTZ. Lots of replacing and service investigation before I got tired of paying $125/hour for "trying".
Ended up getting a new trailer late last year which required a new controller for reasons relating to 2016 technology vs. 2009 technology. I got an aftermarket controller and the IBC no longer governs the trailer brakes.
Shop offered to spend 3 hours to "try to disable" the factory IBC so that I wouldn't see the "service" light, but since the aftermarket controller is controlling the trailer brakes, I can hit the button on the panel (to make the "service" light go away) quite a few times rather than pay $375 and hope it makes the light stop.
Short story is I punted by buying a new controller...can't offer any insight to actually solve the problem.