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I am working on a 1995 F-350 4WD Dually Diesel. I replaced all of the brake hoses and steel lines, new calipers, pads, rear drums, shoes and wheel cylinders and a new master cylinder. Bled the brakes and got the air out. When you start the motor the brake pedal goes right to the floor. Motor not running works as it should, motor running pedal goes right to the floor. I have already changed the master for another new one. The problem is in the front wheel circuit. I isolated the brake fluid to the wheels by pinching off the hoses and then released them one at a time while my assistant (my wife) was putting pressure on the pedal. When the rear wheels were released the pedal held strong as you would expect. When I released either front wheel the pedal went to the floor. As a note this was done with the engine running. So now I know the "problem" is in the front wheel circuit. I am confused....it just does not make sense??? Appreciate your help.
Your description of brakes with engine off and engine running is classic for air in the system, I would bleed them again, closing the bleed screws each time before the pedal is released. However there are other rare possibilities, one is bulging flexi hoses when full brake pressure is applied, another is caliper piston seal roll. This "roll" can occur when the piston drags the seal forward when the brakes are applied and then the seal drags the piston back too far each time.
However I still think it is air.
Yes, the master cylinder was bench bled and the RABS valve was missing when the truck got here. I agree with LAZY K I am still thinking air is in the system.