SNES bindings revert to incorrect config for 8bitdo SNES30 controller

[crunkmasterjoe]

Pi Model or other hardware: Raspberry Pi 3 Model B
Power Supply used: 5V/2.5A power supply from https://www.amazon.com/gp/product/B01LWURJMI/ref=oh_aui_detailpage_o05_s00?ie=UTF8&psc=1
RetroPie Version Used (eg 3.6, 3.8.1, 4.1 - do not write latest): 4.2.18
Built From: SD image used from RetroPie website
Controller used: 8bitdo SNES30 / 8bitdo SFC30 / Wii U Pro Controller
Files:
smb://retropie/configs/all/retroarch/autoconfig/8Bitdo SNES30 GamePad.cfg
link: https://pastebin.com/feHd05T6
smb://retropie/configs/all/retroarch.cfg
link: https://pastebin.com/bXZWxXZr
smb://retropie/configs/snes/retroarch.cfg
link: https://pastebin.com/gsa1nEWL
Emulator: lr-snes9x2010
Attachment of config files: see above
How to replicate the problem:

My two 8bitdo controllers (SFC30 and SNES30) do not bind correctly when being used with lr-snes9x2010. I can't say whether other SNES emulators have the same issue as I don't use any others (but I am willing to test if you find it useful).

The controllers work as expected in EmulationStation, but after loading into the emulator the bindings are all wrong. For example, B is bound to A. The d-pad doesn't seem to respond. Select continues to bind correctly as the shortcut modifier key, but Select+X doesn't open the RGUI nor does Select+Start quit the emulator (Select+Y loads state, although it was always bound to Select+L, and Select+A resets the emulator).

Any attempts to remap the 8bitdo controller within EmulationStation or within RetroArch's RGUI have been unsuccessful. Even if I can manage to remap the 8bitdo controller within RGUI, I'm still incapable of using the menu shortcut of Select+X, and the bindings revert after I exit the emulator and open it again.

I'm assuming it has much to do with the way my .cfg files are set up, but I can't understand the priority with which Retroarch treats these. If someone could shed some insight that'd be fantastic - thanks in advance.

[crunkmasterjoe]

Should it matter than I can't seem to access /opt/retropie/configs/all/retroarch-joypads/? When I connect to my Pi from my MacBook, Finder shows that folder as empty. But if I attempt to drag a copy of 8bitdo SNES 30.cfg from the /opt/retropie/configs/all/retroarch/autoconfigs folder to retroarch-joypads, I get an error. On my PC I can't even open the retroarch-joypads folder.