If the rotor rubs the pad on part of the rotation, then the rotor is warped. Watch it as you spin the wheel and hold a pencil against the chainstay as an indicator. As Expatirate stated, a flat rotor cannot rub part way around.

Try removing the rotor from the hub and set it down on a flat surface like a kitchen table (if it's reasonably flat). Look for a warp.

If you cannot get the rotor to clear the pads without bottoming out the lever, then you have serious warp.