Part of the issue is you have auto select controller set to true, but then you specify your controller setup in the main retroarch.cfg. I’d do one or the other.
input_autodetect_enable = true
or just set this false:
input_autodetect_enable = false
If I was you I would set a button (joypad) to enable hotkeys rather than trying to get them to work on their own. The video above runs through a full example.