Hi therrre,
I've been nonchalantly collecting information regarding gamepad issues that myself and other players have had when using them with FFXI. And for the past few years, I feel I've compiled a somewhat useful guide that players can use to get their controllers working for them.
If you are looking for detailed walkthrough of getting yourself set up with a gamepad, feel free to check out the following links. They contain potential prrroblems you may run into, as well as solutions for many issues you may face.
Have you used this guide and have either failed to find assistance or got exactly the help you needed? Please reply to this post with your controller problem, and if you found a resolution (whether it was through me or elsewhere).
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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)
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.)
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.