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.
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.