In addition to what the OP has posted, I produced several tests on all FFXI config utilities, the EU one, the US one and the JP one (I'm an european player using EU Playonline).
The FFXI Gamepad config utility has 6 available presets
  1. Default
  2. Preset A
  3. Preset B
  4. Preset C
  5. Preset D (only available in the japanese config utility, I think this is for Xinput as well)
  6. Preset E (the new one, specifically made for Xinput)

When you change to one of these presets the registry entries (there are 2 different ones) in the Windows registries get correctly updated and the game correctly reads all the settings of the preset you chose.
The problems arrive when you try to customize those presets.
Let's say you pick Preset E and want to swap two buttons around, or remove a button, or anything else.
These customizations will be correctly written in the windows registry entry, but the game will ignore them and continue using the default setting of the preset you picked up last.
The same happens with any preset, as far as I've seen, not just with the new one.

I've tried to manually change data into the windows registries without using the FFXI config utility, but the result is the same, the game ignores the changes and uses whatever is the default setting of the last preset you chose.


It works fine for the generic settings instead. Hat Switches, Slider, Force Feedback and all the options in that zone of the config software get correctly recognized when you're in-game.