I do not have the NesPi4 case.
So your problem has no direct relation to this one, you should open a new thread.
It seems like the problem is intermittent for me
I don't believe it's a Recalbox bug, it seems to be a problem exclusively for you, as I don't see reports from other users.
but I would need to have some bread crumbs for what to investigate.
Use the latest official version, and the default theme and then check if it happens again, if it happens, open a new thread with as much information as possible.
Also test with another joystick if possible, intermittent errors can be caused by some bad hardware contact for example (I'm not saying this is the case, but it's a possibility).