Try a harder compound brake pad. The heat maybe glazing your pads. A quick temporary fix is to pull the pads and scrub them with a medium grit sandpaper. That will remove any glaze and put fresh pad on the rotor. Overheating your brakes is due to the load exerted. If you are a predominant rear brake user, you'll overload that single disk in short order on a spirited ride (especially 2 up). Use all three disks equally (more on the front is better since 85% of your braking force is there).
I have to remember to use the rear I'm so used to playing on the fronts alone. Hope you sort it out.