In my humble opinion, there is a issue related to the videomode or even the memory, but I'm not getting the point.
I'm not a developer, but, as far as I understand, you're right, the PPSSPP usually has problems with the videomode and the lack of memory, but an RPi4 with 2gb of memory already has enough memory for that, so, the problem in this case it must be the videomode.
Have you tried manually setting the controller for each player?
From the home screen in recallbox hit start and select Controller Settings Then manually set "Input P1" and "Input P2" to the desired controllers. This normally works. I have had to do thsi myself since i keep a SNES controller plugged in via USB but never use it so i set my wireless controllers to P1 and P2.
The only time anything like this happened to me was after editing the config with word/notepad. Using word++ I've never had a problem and more recently I just use recalbox manager via my phone. I know word/notepad used to cause the config to corrupt