I was under the impression that the rotors should always be slightly in contact with the pads....same with shoes and drums.
However, my knowledge of braking is somewhat skewed...every assumption I have seems to be wrong
Yeah, sounds like the rotor is a little warped. Get a new one. They aren't too expensive, and maybe you can find some nice cross drilled ones...maybe a little bigger than your current ones too, if they'll fit.