When the rotors get hot, they expand. If the wheel lugs aren't tightened equally (torqued) they expand unequally. When they cool they contract unequally. Soon those expansion/contraction differences result in pulling parts of the rotor out or in which causes warping. The poster child for this was the early Taurus. In an effort to save weight, ford made the original rotors with a stamped steel center with cast iron outer ring. These would warp if you looked at them wrong. The word finally came out from Ford that the nuts had to be torqued.
The warped rotors couldn't be cut without warping again. Soon all cast iron rotors were on the market. They were more difficult to warp. I never had problems after I started retorquing the nuts after getting tires mounted at the tire store.
Another contributing factor was heat. Again in an effort to save weight, Ford outfitted these cars with 10" disks, which were really toooo small for the car size. When the '96 big brakes came out, I switched my SHO to the later SHO disks. It is hard to believe the increased stopping power an extra inch of disk diameter gives you. No more problems!

It's been my experience that trying to flatten out rotors after they warp is wasted effort, especially when replacements are so inexpensive.

R.