When doing the research on buying a brake controller for myself I noticed that most controllers were for a max of 4 wheels, you have 6. Voltage would be the first thing to check, and can be low from your controller, or the connection, or the wiring, or the distance the wiring has to travel to the brakes. Also check the ground, is it using the trailer ball for ground or a wire?
For a long trailer the wheels might be too far away from the brake controller at the dash to have sufficient voltage. One do-it-yourself option is to re-wire the blue wire (the brake controller wire) in the trailer into a solenoid and pull actual voltage from the coach battery (which will be closer to the wheels). You just have to know that the coach battery will always be charged though. But it would be better to just have voltage from the controller be sufficient.
**edit** actually a solenoid will not work, I realized after the post that the brake controller varies the electrical signal to the trailer brakes and that is how you control the force of braking, where a solenoid would just put 12V to the brakes, Oh, well.