I'm having the exact same problem in other PPSSPP games even with different controllers manually mapped. It's like the mapping is just not there for it to pass the select button. This is even a fresh install on a Raspberry Pi 4 8GB. It still works as a hot key though. The left analogue also seems to be inverted in the PPSSPP menu with you bring it up within a game.

I'm having the exact same problem in other PPSSPP games even with different controllers manually mapped. It's like the mapping is just not there for it to pass the select button. This is even a fresh install on a Raspberry Pi 4 8GB. It still works as a hot key though. The left analogue also seems to be inverted in the PPSSPP menu with you bring it up within a game.