I'm running into a similar issue as well. Through searching through the moonlight github it seems the move to SDL2 has caused some issues with RetroPie. The developer of Moonlight has stated that they wont bother with fixing the problem as it comes from the way RetroPie handles controllers using SDL2 framework. Something around how the buttons are mapped and what the system sees. I'd love more help trying to track this down as well.
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