This is my workaround:-

my /opt/retropie/configs/all/autostart.sh:-

python ~/MFRC522-python/rfidlaunch.py &
emulationstation

my rfidlaunch.py contains:
subprocess.call("/home/pi/nesmario.sh &" , shell=True)
when a corresponding RFID card is detected

this nesmario.sh
contains :
/opt/retropie/supplementary/runcommand/runcommand.sh 0 SYS nes '/home/pi/RetroPie/roms/nes/Super Mario Bros..zip'
emulationstation

this means my RFID script runs all the time, when the RFID card is detected in emulationstation it kills emulationstation, runs the rom as user pi and when the rom has quit relaunches emulationstation.

Thanks for all your help everybody

Update 3: In contact with some theme developers to see if they are interested at all

@guest-001 The original poster had problems when starting runcommand.sh from /etc/rc.local, for which the solution was to change the /dev/tty to /dev/tty1.
There is no reported problem when using runcommand.sh normally, from ES, so I was wondering if you had a similar script set-up - especially since you were talking about noticing an error when a SSH connection was made before ES starts.
I don't know what might trigger your problems, but if you can reliably reproduce it from a RetroPie image, then share the steps necessary to get the error and we can try and see where the problem occurs.

@buzz I'm a completely new to the Retropie scene, so please forgive my stupidity.

If I run a game from a command line I'm assuming that I have to quit Emulation Station.

If I do that will the config file still be used for the system that I am running from the command line to back out of a game (hotkey+start)?

I'm asking because I do not want to unplug my Pi when I'm done with a game...

Thank you in advance!!