My Father in law has a 2006 Ford f250 and a 2004 cougar 5th wheel. He has had some problems with his brake controller/ brakes not working. He can take a 10 hour trip each way with no problems but then...
Here is couple problems that showed on a quick search. I would stop by a Ford dealer and see if they have any tech bulletins or troubleshooting in their system. More issues Ford controller test