I'm pretty sure it's just a matter of becoming accustomed to whatever it is you're using. I've been playing all sorts of fighting games (or any other type of games, for that matter) on a pad for years, and I pretty much have no problem going for hours on end with no aches.
I recently took a visit to my grandparents over in the Dominican Republic, I brought over a PS2 and a bunch of fighting games. Seeing how they never play games, within a few minutes my cousins and the guys over there were complaining about how they couldn't play anymore due to their hands hurting.
Lately I've been trying to get more accustomed to arcade sticks, but I always have that lingering feeling that my input and reactions are not as fast as they would be if I were using a controller. That, and I swear it starts to feel like my hands cramp up after a while. I think with time I'll get used to the stick, I've already seen glimpses of how it can clean up sloppy controller input and just be much better overall for playing these games, but I've got a long way to go..
TL;DR: Should be because you're not used to it, though whether you're just better off skipping pads altogether and jumping right to sticks or not is up for debate XD