Can you send me a screenshot of the exact settings you're using (or, if possible, a project that has the bug)? I'm trying to reproduce the problem, but it's currently working on my end with the controllers that I own.
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!