https://na.nasomi.com/forum/viewtopic.php?f=7&t=192&start=10#p11893 - If your controller's buttons are doing things they shouldn't, or directional pad / analog sticks are not responding or doing things they shouldn't be. (Read here if you're experiencing issues while attempting to configure a new controller)
https://na.nasomi.com/forum/viewtopic.php?f=7&t=4299#p16769 - *For Xbox controllers* If you see "Enable xInput" grayed out on your configuration tool. (Movement, camera not working / triggers responding slowly or not at all, but other buttons do. This issue sometimes appears in earlier versions of Windows operating systems.)
https://na.nasomi.com/forum/viewtopic.php?f=7&t=3971#p15137 - If a controller isn't recognized at all in-game, but it's configured and tested using FFXIpadConfig Tool.
Here are some ideas that may work for you. Read through those topics that relate to your problems. One important thing to note is that you run ffxipadconfig as administrator to ensure the new settings are saved.