Based on the fact that he can use the eye and Kamui a whole lot longer than he used to it could be from training. There's also a chance that it was unlocked from Rin's death, but for some reason he was unable or unwilling to use it (maybe lacked the strength or skill, or save for an ace in the hole) until after the skip. I think once we find out what happens to Rin we will know for sure.
Well, I didn't actually think that second guess was gonna be closer to what happened lol. I hope they got some serious twists coming, or at least something less predictable while still being interesting. It still is so far for the most part.
So it seems Madara knew what was going to happen, probably from being hooked up to the tree and linked to the Zetsus... wouldn't be surprised if he set it all up.