Problems described - If 6 bolt then it seems like they aren't being torqued properly or in the correct pattern. If you have them unevenly or improperly torqued then they will spring a bit when heated during braking.
Warp - fix it. If it continues then fix it correctly.
If you can't keep the rotor within the pad clearance easily then you probably have something else going on. Common causes:
- caliper mounts on the frame are no longer flat and in the correct plane in relation to the axle. Solution: re-machine the mount
- Caliper mounts are indented or scored so that when you line the caliper up while loose it's fine but when you tighten it the caliper moves. Solution: re-machine the mount
- Piston(s) is(are) sticking. Solution: pull the pads, correctly advance a piston, clean it, apply a little bit of DOT grease for DOT brakes or a drop of mineral oil or DOT fluid for the corresponding brake systems. Press the pistons back into the bore and repeat the cycling the piston in and out until they float freely. Clean it all vigorously with rubbing alcohol. re install the pads and push the pistons and pads back as far as they go. Mount the wheel again and advance the pads with several pulls until brake power returns. This should allow the pads to freely advance and then freely retract when the brake is off. It will also allow an out of true rotor to easily push the pad back enough for clearance within a revolution or two.
Like all things on a bike - Disc brake rotors shouldn't be having major problems unless something is foundationally wrong with the setup.