I have the controller set up correctly with the ffxi pad config, but the gaming window does not recognize a contoller is being used.

What controller are you using?

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I've tried with both xbox one and ps4 controllers.

I have a similar problem. I can go to my setting on my PC and it shows that my input is being picked up but when I do the same through nasomi's gamepad configuration tool tests nothing picks up, besides the vibrations.

Went through this yesterday. Run as admin and use one of the default button configurations (you can edit it later).

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Kulgan/Seed
RichFatKids - rfklinkshell.com

That's what I've been doing, but that doesn't seem to help the tool doesn't recognize my controller by default.

Anyway I think you just have to select "Enable XInput"

That seemed to work for me!!!

you need
xbox360_64eng.exe

it's a driver for xinput on hids, usually comes bundled with xbox accessories for windows, but if u don't want the cheezy overlay draggin ur ram down, you only need that driver.

enable xinput in ffxi config > gamepad setup, use alternate setup E.

if you enable xinput you'll likely find that the switchmon app no longer functions correctly, it's not made for xinput.

to solve this you can get the xinputplus ver4.15.2.zip and unzip it and run it as admin, start with selectingtarget program as wherever your switchmon folder is. Then detect gamepad, hit a button and select the gamepad it come from, enable all the drivers, then disable xinput. You'll need to look through the tabs to find all that, anyways apply settings to the switchmon app and it should work per usual.

Gave this advice to many people I known that had gamepad issues and it's 100% the fix, older game vs newer Microsoft things, best of luck.

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!!! Surprise !!!
~not a noob~