Thought I'd reach out to Toyota:
Thank you for contacting Toyota Motor Sales, U.S.A., Inc.
We are sorry to hear of the concerns with the brake controller.
We apologize; as Toyota does not show a Technical Service Bulletin or other documentation describes the condition you are experiencing, we are not in a position to provide specific insight.
You may wish to allow an authorized trailer supplier to inspect the controller to ensure it is installed properly. However, we are not aware of a specific repair or service that would address this.
We have documented your comments at our National Headquarters, where they remain available for review from the appropriate departments. It is through feedback such as yours we are able to monitor and improve upon the quality of our product.
...well that was helpful.