Thanks for testing.
As I wrote during the introduction of this feature, ones you choose to select a button by a button press, Gngeo-gui will wait indefinitely for that button press, making it unresponsive to other input.
Your reason could be it does not recognize your keypad buttons.
It should be a digital keypad, no analog joystick when you use the joystick config in Gngeo-gui.

Could you do a test for me? Unzip the attachment, put it on your phone, activate your usb joystick and run
Let me know what your up/down/left/right button give as a response.