@mitu I was having a similar issue when going from clean install of RetroPie 4.7.1 (Raspberry Pi 4 image from RetroPie) with some 8BitDo controllers. I cant remember if I also had this issue with those cheap iNNEXT SNES usb controllers.

@Dagna The beta image at: https://retropie.org.uk/download/
Might be unrelated, but I've had random issues with this build and previous ones, but devs can't reproduce it. For example, ES wouldn't save my inputs until I re-installed ES from retropie-setup. Maybe it's my bad card (a few months old) or the card reader's bad.

Backup the ROMs and BIOS folders, the \\retropie\configs\ folder - the emulationstation folder contains your collections and ES settings/own themes`. Here's a topic discussing this in detail - https://retropie.org.uk/forum/topic/16866/.

@BJRetro Yes everything works good! Thanks for the extra info on Naomi/Atomisware!!!
Guilty Gear X 1.5 and Fist of the North Star works great.

@asici2 Yes, the feature is only available for lr-fbalpha.

FBA is optimised for Capcom fighting games so lr-fbalpha is the recommended arcade emulator for the Street Fighter games. You will need to find a new romset as lr-fbalpha uses a different one to MAME. More info at: https://retropie.org.uk/docs/FinalBurn-Alpha/

@defenderdev Ok I'll give it a try thanks

In my case, it was because I registered the PS3 dualshok controls, using the xbox360 driver ... In emulationstation it works ... But in RetroArch it does not.
The solution was: uninstall the xbox360 driver and re-activate the ps3 dualshock official driver, when rebooting ... Resigne the buttons in emulationstation, I recognized as ps3 dualshock command and I work the retroarch controls in all the emulators.

@orangewaffle

Ok, reaching home, i got the information needed:

Pi Model or other hardware: (B, B+, 2 B, 3, X86 PC etc..) 3 Model B+
Power Supply used: (If using a Pi) Samsung genuine adapter, 2A
RetroPie Version Used (eg 3.6, 3.8.1, 4.1 - do not write latest): 4.3
Built From: (Pre made SD Image on RetroPie website, Berryboot, or on top of existing OS etc.. - please provide the filename of any image used) Pre made SD Image on RetroPie website, but i can't remember which one
USB Devices connected: 2
Controller used: DragonRise Inc. Generic USB Joystick
Error messages received: -
Log found in /dev/shm/runcommand.log (if relevant): -
Guide used: (Mention if you followed a guide)
File: (File with issue - with FULL path): -
Emulator: (Name of emulator - if applicable): can't say, because i can't get into emulator options (nothing happens if i press any button during game load)
Attachment of config files:

After replacing a 1A charger with a 2A one and giving the setup a one day rest, 7 out of 9 buttons work now, instead of 1. Top left button still does nothing, as well as the hotkey button.

In the weekend i will try a clean install of the latest retropie image and keep this post updated.

Check this out and you can get even 4 Atari joysticks connected with a single USB. Works great with my Raspberry Pi 4 and emulation station. https://www.icode.com/atari-joystick-usb-adapter-design/

@loonyboi Thanks! I wasn't sure if you meant to mirror the controls by ES' UI or at file system level by copying their config files. So if I understand you correctly, setting them up identically in ES does suffice.

I'm having the same problem where none of my controllers are working in game, however, I know what you're talking about, as I had that same thing (with the having to basically hold all the buttons to get it to open the remap screen) happen to me. Unfortunately, I have no idea what caused it, and I was only able to fix it by doing a clean install. If it's any consolation, since the install I haven't had that problem (just my current one where my controllers aren't working in game)