The difference was that Chan choked a bit gave away the gold at the Olympics. The judged loved him, and he was an exceptional skater. Whereas the judges never favored Stojko, and never would. He had to fight for every medal he got, and usually won based on technical. At the '94 Olympics it really could have gone either way, as Urmy and Stojko had similar tech content and each made a mistake. But the judges preferred Urmy.
Then, in '98, Stojko had a groin injury. He couldn't land the quad, and it was quite a feat that he managed to get through the whole program without falling. He was clearly in pain during his skate.