Ah, I've never had that happen, I think it has happened to somebody else before. As typical Leo would probably know the path to take to resolve it.
Only solution I have to brute force around it would be to use something like xpadder, but it definitely sounds like it's client side.
I think I fixed it.
In that folder there was a file called FFXiPadConfig, which just booted up the controller portion of FFXIConfig. Everything registered there, miraculously, and now I'm good to go! ^_^
Also a big thank you to
Josi for help with the Seasoning Stone and the encyclopedia's worth of info he chucked at us! EXTREMELY helpful, thank you so much!!