Mates evo had the same issue, we had tried to figure it out for literally months while at pukekohe and taupo.
Turns out the new pads he had were too high end and not able to seal with the heat generated, the glue? compound in the pads were leaving resin on the discs.
By this stage we had tried just about everything but the pads. (doh)
Replaced the endless pads (cant remember which ones) with less hardcore version, problem solved.
although in your case sounds like warp/not alligned brakes/rotors. have you tried bleeding your brakes latley uncase theyre not applying pressure uniformly?