I went through this nightmare a few years ago. I had a set of Galfer rotors and pads installed. All good, and wore them out to below spec. When time to replace, I bought new pads, rotors and new Suzuki OEM calipers. I didn't want to hassle with rebuilding, and the bike had about 75K at the time, so everything was replaced.
A month later, the left rotor was warped real bad. If you grabbed the lever at speed, the shaking was terrible. I called Galfer and they said to send the rotors to them for inspection. They confirmed that one was way out of spec, and they sent me a new pair. I had bought a set of Brembo full floating rotors to try, and saved the new Galfer for a rainy day.
The new Brembo rotors and pads were installed, (and paying the mechanic bunches of money again), Guess what? Yup, warping of the new rotors in about 3 months. F***. What was causing all of this?
It turns out it was a defective caliper. Hydraulic issue would not let the pistons retract completely, which would drag the pads ever so slightly, causing heat, and the warping the rotor.
Only after doing a spin test on each caliper, did we figure it out. Take off one caliper, spin the wheel and count the rotations, and then do it again on the other side. It was quite obvious after that what was the problem.
I had the old calipers rebuilt after all, and the problem went away, but I was out a bunch of time and money, and no one in the food chain would warranty, or refund my money for parts and labor because the time and mileage elapsed was too long.
The problem was very slight, and took time to warp the rotors. The lesson I learned is that just because it's all new parts doesn't mean it will be perfect.