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@davisp See if this helps:
https://forum.recalbox.com/topic/24280/n64-graphics-ok-on-first-start-only
Sowas passiert, wenn man eine alpha Version benutzt. Installiere 4.0.2 indem du die root und boot Datein aus dem Zip nimmst und ind /recalbox/share/system/upgrade reinkopierst und neustartest. Nachher kannst du über unstable aktualisieren.