That can't be the problem because all other settings in FFXI config work normally. Also when I went back to the XBCD driver and turned off xinput I can reconfigure the controls as before.
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Which OS you are using? I am using Windows XP still. And I know FFXI works best with Windows XP simply because it's a very old game... lol
I noticed that even if it works properly the button numbering used by FFXI doesn't match the one used by Windows itself.
I'm on Windows 10 and I'm having the same problem. I could definitely see this being OS related. Incidentally, the button selections do work for PlayOnline, but that doesn't support Xinput so that's probably irrelevant. (You could always use the buttons normally on Xinput, they're just numbered differently.) FFXI itself seems to completely ignore your button setting choices.
Sigh, they got my hopes up and then broke something else... Really hope they patch it so we can set our buttons, having to use start and select for macros is far more preferable than having my confirm and cancel inverted..
I play using the Japanese buttons layout so it was a annoyance for me that it actually worked properly (I had to invert the buttons manually) but the changes actually stickied properly.
That's how I use my controller:
Y=HUD
X=Menu
B=Confirm
A=Cancel
The USA XBOX 360 has the buttons set this way:
Y=HUD
X=Menu
B=Cancel
A=Confirm
This is weird. >_> Is there any way we can experiment to see what's causing the problem?
Reddit has a fix involving removing the xinput.dll file and then reconfiguring controls again.
Only way I've found to counteract this is to use InputMapper in exclusive mode and remap the buttons on my PS4 controller.