I actually heard, and I think it was on this forum, that rotors are very hard to warp. What happens is that the brake pads wear in a non-uniform fasion, and you get the same result as if the rotor was warped.
Anyhow, in regard to the original question, might it have something to do with the traction control or ABS? Does it occur as you are coming to a stop? Or after you are completely stopped?