The trouble isn't really that your rotors are "warped," but that they have become of varying hardness around their circumference, which causes the pads to abrade them to varying thicknesses. This is caused by an occasional hard stop, which heats the rotors substantially, followed by the continued application of the brakes, which causes the heat to be trapped in the portion of the rotors that is under the pads, but allows the heat to dissipate from the rest of the rotors. You end up with slight variations in heat-treat. This is then followed by a driving style of light brake usage which is ineffectual at removing the high spots from the rotors.
As a first step, I would recommend that you try on your OEM rotors the bedding-in procedure for new aftermarket rotors. You'll need to find someplace out in the country with long, straight, low-traffic roads. The goal is to get them hot, and then let the heat dissipate evenly.
Get up to 60 mph, and then brake as hard as you can down to 5 mph. It's important that you don't come to a complete stop. Do this ten times in a row. Let the rotors cool by driving without braking for about 10 minutes. Repeat the series of panic stops and give them a second cooling period.
If the problem persists, I cured my brake problems completely by installing aftermarket ART rotors and PFC pads.
