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Did you enable the root account and login as root ?
You should install from the "pi" user
It would be easier to do a fresh install than debugging this imho, as you will want to reinstall from the correct user.
@UDb23 yeah it's a little hidden in the wiki, perhaps I'll make it a little more verbose:
For reference: https://github.com/retropie/retropie-setup/wiki/EmulationStation#my-es_sytemscfg-is-being-overwritten-on-updates
