I’m having the same problem, but with a ZD USB Encoder (board adapter for real arcade buttons).
With Retropie 2.3 I can configure the button mapping fot the emulationstation without problems, but with newer versions of retropie such as 2.6 I can’t configure.
When I start a fresh installation of RPIE it asks me to hold a button to configure controls, this part is OK, I hold a button and start mapping the buttons, the problem begins when I have finished configuring the button mapping, it take me back to the top button of the list (up axis) and it stays there as (Axis -2) and I can’t move down or up to the list so I can reach the “OK” button to save the config.
Configuring a keyboard for this feature is ok, but I need to configure the arcade stick and buttons for this project.
Anyone is having the same problem ?