How sure are you about the wiring? Do the flashers work without braking?
I had some issues too when I rewired all the cables to the lights. They were caused by a bad ground on the steering column. So check all the grounds!
Edit: Or maybe just a bad brake switch. you could test it by taking it out, and connect it directly to a bulb from the battery. and also connect the -side.
Last edited by Raoul; 02/09/2015 1:21 PM.
