Thank you for your answer. Actually I played a bit with retroarch.cfg, with someof the controllers pluged in in differents usb port and it seems to work now ! Not exactly sure what really made it work though :)

My guess, the gamepad is being read as port 3, which often won't do anything in most games since they're 1 or 2-player. What you can do about this:

Open a game, and then open the RetroArch quick menu with P1 Select + X. Go to quick menu > controls > port 3 controls > mapped port change from "3" to "1". Close the menu with Select + X again and test your gamepad. If it works for P1 control, open up the menu one more time with Select + X and save a core remap file. You will have to repeat this once for each core/system.

What model of SNES USB controller ?
If you use jstest to test your controller, are the D-Pad left/right inputs recognized separately, or they overlap other buttons ?

If anyone else has this problem, it seems that InputAutoCfg.ini is what you are supposed to edit. Changing plugged to false just gave a no controller message. Since I didnt see any section for order, I changed the order of the controller configs but that didnt change anything. However just deleting the nes gamepad section worked and now my bluetooth controller is controller 1. It also stayed that way through restarting.

What exactly is the error/issue ? Is the controller not working ?

As @sirhenrythe5th said
3rd party images
are not supported

As detailed in https://retropie.org.uk/forum/topic/3/read-this-first.

Please add more info about your system and setup, as detailed in https://retropie.org.uk/forum/topic/3/read-this-first.

@simpleethat they should have. Both lr-picodrive or lr-genesis-plus-gx mapMode Select.

@markyh444 Okay. Mitu gave me a starting point to work from so I will take his advice and go from there. If I need further assistance I'll be sure to take the time to collect the necessary information first. Thanks for your responses.

@lostless Sir/Madam thank you SO much. SO Much

I was having a NIGHTMARE sorting this key out - i had read on MANY threads and forums about the Start+Select combo. But you are the first to say EXPLICITLY that the hotkey MUST be pressed with something to exit.

Mapped PS button ...sorted, done, solved. I dont know you but feel i owe you a drink at LEAST one !!

I have managed to get it operating correctly. I just need to configure the buttons now. Thank you.

After spending the weekend thinking about which procedure was done wrong, I remembered that I performed many installations and updates hoping to fix the problem, so I downloaded a clean .img and installed it again. After reinstalling the OS the control worked correctly, thank you anyway.

@mitu Thank you, I'll try this out and get back to the community.

@mariobros_54 As @mitu says. ES only displays a system that has roms in its rom directory.

@aj36601 I had a similar issue with my 2 player setup. I found that once I just swapped ports on the usb, that it stayed fixed.

I'm sorry, this was a total newbie question. I'm figured out about TAB in stella since. I also gave up on the steam controller and bout an 8bitdo one. Seems the support isn't quite there for the steam controller yet.

@mitu Sorry about that. I wasn't sure how to post the log file. So I ended putting some soldering some pins on it and putting it in a freeplay zero. I wiped the sd card and added the freeplay modded retropie (That was before I saw your post asking for the log file...). Weirdly enough a somewhat similar issue occurred again. The buttons stop responding and the pie pops up errors. Since I wiped the previous log and I can't access get my keyboard to work on the gba I don't think I can provide much to you. I talked to Ed from Freeplay and he suggested some things to try out. If it doesn't work I'm going to just try out a new raspberry pi and see if that's the problem. Thanks for taking the time to try and help me troubleshoot.