if you're using the stock brake disc check if the brake cam is pushing one brake pad against each other without applying enough pressure on the disc.......this is why with the minimum wear on brake pads can cause that due to thickness of the disc........

with the ventilated disc made by kawahara (I also think the mtx3 prospec one will fit) you won't get any trouble when braking no matter the pad you choose (black, yellow or blue)