i don't think it would be that from what hes saying though, if it was the master cylinder it would do it cold too...if he pumps it and they work fine sitting still after pumping repeatedly then only fade after they heat up, then work again when cold its almost definately going to be hes boiling the fluid...in other words, it would stay spongy or would get spongy just sitting there and pumping them, because that would mean the fluid is getting past the master cylinder check valve or piston
did you know brake fluid actually absorbs water to an extent ? Weird huh ? anywyas that could be the problem, but with an aftermarket pad that has like 25% the coeficient or friction of a stock pad, you will have alot less heat and changing brake fluid although i never do so i'm a damn hypocrit, should be regular scheduled maintenance, ive heard and read that ALOT...
i would cheak your pads, clean your pads, calipers and rotors, top off your fluid and bleed your brakes just in case there was some air in there, then if like i said they work if you sit still and pump them aboout 30 times but once you ride like the wind and brake hard they fade then go back again when cool, you are definately boiling or have contaminated fluid...
if they fade without a spongy pedal it usually meanse you are 'glazing' your pads or heating them up to the pont where they were formed at, in that case your lever will be stiff still, it will just fell like your brakes have oil on them or something...
belive me, i did my homework on at a young age, never had a problem on the dirtbikes, but when i got my first car and the brakes got spongy and started smoking, i knew i had to learn something, lol