I recall seeing an interview with Tony sometime after he sent Burns to the pen. He said he and the coaches felt they needed more competitive fire in the rotation, and Andrew Lindsay was given a chance because of his competitive fire. I took that to mean - at the time - that the staff didn't feel Burns had a competitive fire.
Perhaps that got back to Burns and caused him to be angry at Tony in a way that he just couldn't forgive. Either way, something lit a fire under him for the last part of the season and post season.