I have the controller in my 2nd post. A seperate user in amazon review confirms it to work with the retropi (I also confirm, see below). My first thought as well that it might have been the controller. However I also get the problem with a generic microsoft keyboard with no controller attached and vice versa.
In version 2.6 both devices are seen, both work, and no configuration outside of mapping for emulationstation specifically. I know this because it doesn’t ask to map x and y and they both buttons work in the retroarch backend out of the box.
Is there a log or something you want me to gather? I am willing to try re-flashing so it can be addressed. I would like to stay on the current version if possible.