Not Square-Enix support, obviously, but...

To add to Rhaervis' questions: are you running the Steam or non-Steam version of FFXIV (or running the non-Steam version through Steam)? If so, Steam's also potentially processing the controllers; it might be worth toggling that (try without using it if you are using it, or with using it if you aren't using it) just to see what happens.

(Note: so far as I know, the PS4/Xbox controller configuration/mapping option can only be enabled from the Settings screen in Big Picture mode, which is sort of irritatingly non-intuitive.)