Not Warped Rotors... What Is It?
 

I have a 2000 Boxster S with factory rotors and pads. Have done several DEs with no issues. This weekend I experienced the followingIn the middle of day #2 the following started to happen:
When the brakes were hot and I was doing heavy breaking from high speeds (example breaking from ~ 115 mph the car felt like I was braking on a "washboard" surface, meaning that the car became a bit unstable and started to "wobble"

This was NOT the ABS, which feels different, I also did not have brake fading and I had pretty much the same brake distance as before, so the brakes generally still worked great. And it only happened after a few laps when the brakes were hot.

When the brakes are cold everything feels normal. I checked runout and have 0.001" or less on each rotor, no cracking or signs of any pad material buildup. Pads have at least 8mm of material left.

Ideas?..

My guess is that the pad material was being deposited unevenly on the rotor when very hot, then scrubbed off on slower corners and when driving normally. I would suggest trying a higher temp brake pad.

Are you sure they are not warped? What method did you use to check? Loosen the lug nuts and re-torque them properly. Uneven torque on the lug nuts can cause this.

Check the torque on your brake caliper mounting capscrews? (Make sure not loose)

I mention it only because I recently noticed mine were a lot less torqued than they should be. They seem like pretty important fasteners to not come loose!

Hub Centric
 

you might explore this route

Mr. Stone is correct imho. Solve by fitting top quality pads. Hawk, EBC,Akebono ?Others will mention their favorites.