the same file can be downloaded directly on nexus when the warning upon download it here too. hope that helps https://www.nexusmods.com/finalfantasy6pixelremaster/mods/101
i cant seem to replicate that problem. try disbaling steam input plus on the setings make sure to turn on the option for generic controller support and turn off switch layout
if you have switch layout option on steam.. probably you should turn it off.. this is design for X-input. turning that option off will default the controller on x-input.
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it here too. hope that helps
https://www.nexusmods.com/finalfantasy6pixelremaster/mods/101