you are either dragging the brake or using it so much the heat builds up faster than it can be dissipated. you are boiling the brake fluid causing bubbles which makes the brakes fade, when the fluid cools down, the bubbles go away and the brakes return. it is pretty common for people who drag their rear brake, I know from experience
Also if you are running an aftermarket pipe, many of these run close to the rear brake resevoir and can heat it up further. I run a braided line up the side of the frame as a resevior that keeps it nicely away from the pipe. If you look at pics of Scott Summers 600's it appears he may have done the same.