Well, there isn't really a need to advertise that there's a configuration menu... if you read the screen it says B Button = Settings or something like that. Also, it's not that it spams the button (at least, it's not supposed to, even if you have only one game) but it does seem like the autoboot was enabled. This would be caused by loading a game straight from an usb loader with such option enabled, or maybe a previous attempt. You can stop the autobooting by pressing B (it should say so in the screen if that's the case B = Stop Boot)
In any case, I'm glad you could sort it out and enable the HID option in nintendont.