Real quick solution that I found while scouring messageboards:

So I had the same issue using the Xbox one controller and the keys not inputing while in game. I have the Xbox one controller unplugged when I start the game. Once the games goes full screen at the accept/decline page I plug the controller in before I select agree. You should be able to use the D-pad now as well as the left and right arrow keys to switch between the 2 options and if they both work there you should be all set in game! If you forget to plug it in before hitting agree (which I still do occasionally) it's kind of annoying because you have to exit and start over, but to me it's less annoying than having to delete an update from Windows.

Anyway this has worked for me and I hope it works for anyone else having this issue.

FYI - Stole this from Steve12824 at

http://forum.square-enix.com/ffxi/archi ... c8cc45446b