Perhaps that controlled power to the fan header. Back in the days when 6800RPM Delta "Black Label" fans were the rage with overclockers, many people experienced the problem of fan headers dying because they weren't designed to cope with the amount of amperage that the high RPM fans were drawing. Perhaps your old case fan had a short in it.
Last week one of my friends plugged a brand new NMB fan into a motherboard header. The fan is a super quiet design and was sold by electronics overstock places, and had a 3 pin plug similar in size to, but not identical to a typical 3 prong header on a motherboard. Problem was that it wasn't wired the same, and I don't think the third wire was even an RPM wire. Well, he plugged in this fan without rewiring it properly and the fan motor started smoking. The rest of the system wasn't damaged.