Another suggestion:

I think when you reinstall the game, it doesn't remove your user folders? Your specific character data is still there if I recall correctly.

I'd try just deleting all of your user data from the FFXIV folder under 'My Games' and the login to the game to create a fresh set. That would clear out any potential corruption in the settings files that control your UI and controller data.

(of course, make a backup copy if you have settings you want to keep - but you may risk introducing the same problem if you copy the old data back...)

If the problem is not happening in Windows and only when you're in the game, then it has to be a configuration problem with the game settings.