Your 3 line question leaves a lot of information left out for someone to really help... ... but here is a start... .
When a rotor is over heated it can cause brake pedal pulsation. The overheating process causes it to warp and thus not run true to the center line of the bearings... . Once this occurs the rotor is trued and all is well...
When a new set of pads are installed, and the calipers are not inspected correctly, one caliper might be dragging and this will cause the same problem... . the rotor overheats and warps...
When the boot between the piston and caliper is damaged, dirt will get behind the boot into the piston and will not allow the piston to return correctly... . this slight drag can and will cause that rotor to over heat and cause it to warp... .
Also, some new rotors are shipped without bearing races in them, and if the bearing race is not seated correctly and out of true condition can result...
In addition, all rotors should be trued up, even when new after new races are installed... the CNC equipment used to manufacture a rotor might not be spot on, thus allowing the rotor to be out of true...
I'd almost bet that you pushed the piston back when you installed new pads instead of bleeding the dirty brake fluid out of the system... and sometimes this dirt can cause the piston to not return correctly... this dirt gets between the seal, piston and bore of the caliper, and pressure will push the piston out but once your foot is off the pedal the quick return of fluid sort of pulls back the piston just a fraction of an inch and it no longer touches the pad, thus the brakes are free... . one piston is dragging in the bore overheating one rotor...
Last, severe damage can be caused by this dirt pushed back into the master cylinder... .
So to really help let me ask these questions... .
1 - We're the first set of factory pads worn out? if so, how, if not why were they replaced?
2 - did you bleed off the dirty brake fluid when you compressed the pistons?
3 - did you inspect the boots that cover the piston and caliper for damage from heat, or dirt, or just being not seated in the bore?
4 - Why did you replace the pads the second time? The first set should have been fine!!
5 - were there races in the new rotors, and if not, why did you not turn them?