I had a problem getting the FFXI config tool to recognize my wireless Xbox 360 controller on my PC. The controller would vibrate, but no other inputs were recognized (buttons, thumbsticks, etc.). After some trial and error I figured it out. Basically, I also had a joystick plugged in (I had been playing a space sim). When I unplugged the joystick and restarted the FFXI config tool it all worked perfectly.
So, it seems the FFXI config tool will latch onto a particular controller and other controllers will be ignored. It doesn't seem to matter which one you tell Windows is the "preferred" or default controller, FFXI makes up its own mind on that.
Therefore, unplug any and all controllers, or anything Windows thinks is a controller, except for the one you plan to use.
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