The only thing I can think of would be the amount of pressure that's involved in the process...

If you're masturbating by wrapping your hand around the shaft of the penis, that would probably put more pressure on the urethra and its contents during the actual ejaculation. If most guys are like me, they probably tend to unconsciously squeeze even harder during the crucial moment because they know from experience that it will make their semen fly even further away if they do. (And what guy can resist that kind of thrill?!)

However, there's probably wouldn't be as much pressure pushing in on the shaft during intercourse, or during frotteurism (not sure about the spelling there, but I'm talking about when you masturbate by rubbing your penis against something else, without using your hands). I've tried it both ways, and the latter doesn't seem to hurt nearly as much as I when I use my hand...

Stands to reason, doesn't it, that if you're squeezing and constricting the only exit route, the pressure on the fluid inside would back all the way up throughout the entire system, including the epididymis... Maybe that's why (manual) masturbation is usually more painful for most guys...?