Trailer Brake Controller will limit engine RPMs?

"It's ALWAYS worse when the brakes are very hot too. Like after being on the highway for a long time."
This doesn't sound right to me. The brakes should not be hot while running down the highway, unless your riding the brakes, have bad wheel bearings, driving in heavy stop and go traffic, or the brakes are set too tight.
You may want to have your braking system checked out by someone who knows RV braking systems.