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I’m not sure how you wired it up – is the Arduino acting as USB HID device to the RPi?

I built a pinball controller using an Arduino Leonardo as USB HID “Gamepad”. That way I could use analog axis, tilt sensor, and of course some buttons. I use it for my pc pinball simulators and not configured for retropie, but I expect it not having the issues you describe, at least jstest looks all good.

If you want to turn a Leonardo (or Micro) into a custom USB HID, you have to change some C header files and create a suitable HID descriptor.