This may be a Steam issue where Steam is overwriting the controls. I tried playing a game but discovered my controller's custom keybindings were ignored. When I rebound them through Steam, they worked the way I wanted. Hope this helps.
Viewing post in Custom Controls (RMMZ Plugin) comments
It's working!
Steam seems to be related. I tested the new version with a deployed project (Steam closed) and the overriding works perfectly. Also with the new version, in playtesting mode now the gamepad behaves just as if the puglin were disabled for me (No longer the advance dialogue button changes from A to Start)
Thanks reflector88!