I had the same problem. The solution: understand how recalbox works; 1 joystick configuration per hardware. That means if you use two identical zero delay cards, the system will create only one configuration for both cards.
You must connect the wires from the card to the buttons on both controllers following exactly the same order. The same occurs if you connect a 3rd or 4th identical zero delay card.
After that, you should configurate only 1 controller on recalbox and all the others will automatically be set up.
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