I think that the reasons could be that: The prophecy did not mention the heroes who defeated Alduin would be helping the Dragonborn defeat Alduin again. Since it didn't happen correctly, he would returnto fulfill the prophecy. Or, all events in the scrolls will come to pass, no matter how long they are delayed. Finally, the Scrolls influence everything in the universe so what is predicted WILL happen, since they are sort of possesing the power of Aedra, and essentially are parts of the universe's creation.