Bump hoping someone else has experienced this and has some pointers. I have been busy moving and haven't had a chance to play with the pi all week.

This worked perfectly!! Thank you.

If you post up the info requested at: https://retropie.org.uk/forum/topic/3/read-this-first you'll likely get more responses and help.

As you are using 4.0 make sure you have installed the ColecoVision emulator:
https://github.com/retropie/retropie-setup/wiki/Updating-RetroPie

@Arcuza The real fun starts when you enable "save config on exit". LOL!

Try to read this thread carefully:
https://retropie.org.uk/forum/topic/2199/specific-retroarch-emulator-settings-are-being-over-written-after-i-quit-the-game

How come it's only the triggers/shoulders that didn't work...?

Also, why does it register as 6, 7, 8 and 9 and then not even register those lines to the cfg file?

Anyway, thanks guys, you are legends. Been trying to fix this for days

@caver01 awesome detailed answer.. thanks for the feedback!

Thank you! works again!!

@megasweet : lets move this conversation to the GitHub issue

It was me that was blind... I found it... =)

It all has to align with the ROMs and BIOS being compatible in the NeoGeo or Arcade ROMs folder. I cannot link you to any files that I am certain are compatible but do some searching and forum hunting at some emulation sites. I been having good experience with the latest NeoGeo game files and BIOS. No need to go back to older stuff IMO.

https://github.com/retropie/retropie-setup/wiki/Transferring-Roms

I fired up other games on lr-FBA-next last night and the overclock I did for Metal Slug was saved for the core across all games. Not sure how this affects anything if it's worth just leaving alone.

NM...apparently I didn't look close enough while poking around in the setup script. :-\

@mattw24 It seems that you have no hotkeys to savestate, and this is why it is not working.
Try it without the trailing 2> /dev/null (this let us see the error messages, if they exist). Just:

grep -R save_state_btn /opt/retropie/configs/all

I suggest you to reconfigure your joystick in emulationstation: press Start and select CONFIGURE INPUT.

Reading suggestions:

https://github.com/RetroPie/RetroPie-Setup/wiki/FAQ#how-do-i-change-which-buttons-to-press-to-exit-an-emulator-with-a-controller

https://github.com/RetroPie/RetroPie-Setup/wiki/RetroArch-Configuration

I'm sure your problem is very simple to solve, and I'm sure that if you read and understand the links above, you'll solve it easily.

Thanks for all the help @Floob. I noticed while setting up a second controller that emulation station seems to reasign A and B any time you set up a new controller and go in and out of an emulator. Is this a bug if so I would think it needs to be fixed not to cause anymore confusion. Seems to only happen with these controllers. I fixed it by manually updating es_input.cfg but I had to do it twice because of this.

ohhh baby! that 4.0 is awesome.. a lot cleaner interface than that of the 3.x version.

I found a different rom that works perfect.