I have just finished building two arcade controllers with a Zero Delay Arcade USB Encoder Board in each.

I've just burned the  retro pie 128GB image on my 3Bplus.

The two gamepads are detected in emulation station, and I am able to configure them both on startup. The menus/navigation work perfectly after configuration.

When I select a game however, I see the informational message to press A to configure controllers, the game loads, but NONE of the preprogrammed functions are active, and pressing A doesn't do anything.

With a keyboard, if I press escape I get to the game select menu but the controllers no longer work.

Similarly, if immediately after configuring the gamepads, I restart (using the menu) the Pi, configurations are not saved and I have to reconfigure the controllers every time.