Over time a lip will form on the brake rotors because the pads do not contact the entire surface of the rotors. I had a lip on the inside and outside of each side of each rotor about 2 mm tall. One of my pads had less that 2mm of material left on it, so the lip made contact with the backing plate, causing a grinding noise. I replaced pads and rotors on the front axle.
You said you already checked the pad life. Are you certain you looked at all four pads? With only 2900 miles to go on these pads, I would have ordered new pads and rotors already. I bet changing them will solve your problem.