It would take a lot of hard heavy braking in order to warp the stock rotors, and the stock pads would deteriorate long before that would occur. You need to "re-bed" the pads. Old rotors need to be turned before doing this to create a clean surface. If you change the pads or rotors, you need to bed the pads in. Basically, heat them up so they mate with the rotors as best as possible. This is done as described by The Black Box, 5-6 heavy hard brake runs from 60MPH to 5MPH and then let the brakes cool via driving around and not using the brakes. This puts an even layer of brake pad material on the rotor and provides the optimal braking surface.
What you are experiencing is pad deposits in the rotor. This causes uneven braking surfaces along the rotor, making it feel like the rotor is warped. I liken it to what a record would look like, or a wavy washer. Stoptech has a good write-up on
"warped rotors" and also on
bedding the pads in. The only time you should ever have to replace the rotors is when they are too thin per your local safety standards. I replaced mine at 120k miles as they were too thin to turn.