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...
Check the ground connection on the connector! Verify that both ends are correctly grounded to the FRAME and both battires are correctly grounded to the FRAME. Bad grounds cause way more issues than they are given credit for.