I would also like to know...
Soul Calibur has a 1S version and a 4S version, and I cannot find any differences between them.

Deleted /opt/retropie/configs/all/retroarch.cfg, then reconfigured the input in ES, now it works. ¯_(ツ)_/¯

@nialithe My best guess is the permissions are messed up on your rom directories (this can happen if you copy roms/folders as root). The simplest way to fix is to run the following from from the RetroPie_Setup script: C Configuration / Tools -> 821 resetromsdir. This will fix permissions and you should be able to save. Another possibility is that you disk is full, but you'd likely see other problems if this were the case.

Perfect Thanks il Will try

Great! I was looking exactly for thi ssolution, coz I'm running RetroPie via BootBerry and it is no possible to use raspi-config. Thanx!
For other users:

Boot to RetroPie Enter Shell by Ctrl + F4 cd /boot sudo touch ssh Reboot, done!

@zarrath https://retropie.org.uk/docs/RetroArch-Configuration/

Thumbs up ;-)

@edmaul69 I know normally you're supposed to just wire the positive and negative ends to the appropriate pins on the control block. They're specifically marked. But im not sure what to do at this point. Thanks for your reply

@Drakaen391 the way retroarch is set up it is probably better to setup like a super nintendo controller and then swap the a and b controls for emulationstation. All emulators using retroarch were set up to set the controls correctly based on that setup and orientate the buttons accordingly

@miran81 there is probably stuff you have to do to get it to display on the lcd. You need to look for a guide for the screen you are using.

So i've finally got further with this issue. I've removed retropie from my SD card and reinstalled it. Added the correct driver and set every GPIO pin in de conf file to 2 so my config now looks like this: gamecon_gpio_rpi map=0,0,2,2,2,2
Interesting enough now all of my controllers seem to work without the 5v mod or extra wires whatsoever. I've attached the NES pad to the PAD 4 pin. The only thing not working right now is in-game. The NES controller works in the menus of retropie and emulation station but not in an actual NES game. Going to figure that out next!

@edmaul69 Yes i have a mouse, gamepad and keyboard attached. It was running on HDMI just to take this picture. The mouse is above ESC button.

@dsfrancis that probably wont work. Rename a file from .bin to .sg . Then restart emulationstation and test. Will probably work that way.

Answered the question myself by just running part one. It seems to work, but man satellaview games are odd.

Thank you for reply.

Hey rbaker, thanks for the response. I ended up reflashing the sd with a new image of retropie. Previously i had retropie installed manually on top of raspbian. This is fine because i really dont use the pi for anything but gaming. I'm sure one of the scenarios you mentioned was the problem. It seems like probably the folder structure was corrupted at some point and no longer being correctly picked up by retropie.. i guess =)
Reflashing with the newest version of retropie worked like a charm, all my original roms work. Now im on to trying to get metal slug 5 to work correctly! xD

@edmaul69 My guide was really just taking the steps from the Raphnet site. Raphnet's site tells you to go to the Raspberry Pi site for some of the steps, so I just put them all in one place.