Hi Sage,
At the moment the settings should work with input from the keyboard and mouse click buttons. I haven’t looked into how autohotkey works, so I don’t know what the problem is with the joystick you are using. But I do know that the key presses used for the EyeX Interaction are hooked on a low level and then consumed. We need to consume the key presses so we don’t have context menus pop up every time the Applications key is used to Direct Click something. Maybe that could be a clue to why it is not working?