Kind of late but just read this, believe it or not the number 1 cause of warped brake rotors is improperly torquing the lug nuts. My 99 LS calls for 76 ft lbs and all vehicles should be done in a cross pattern. There are untold hundreds of not so honest shops that will over torque lugs on purpose. The thing with the improper torque is; you don't get warped rotors right away, they typically will warp after a fairly hard stop which causes them to get good and hot. I'm not sure this is your cause but I'd have to agree that the master cylinder doesn't sound logical to me either. On the other hand frozen caliper pistons could cause it but typically you will notice the car pulling when you apply the brakes and believe it or not it will pull to the opposite side of the frozen caliper. Good Luck