partially resolved. i had a setting enabled that was preventing new games from coming in via the scrape options.
I see the problem.
The problem is you have enabled ParseGamelistOnly - which will mean it doesn't scan for roms and only shows items from scraped gamelists. Hence your roms are not showing up.
https://github.com/retropie/retropie-setup/wiki/FAQ
Parse Gamelists Only: If on, it will only read the roms you have scraped, so if you add any new roms it will not look for them unless you turn this back off. it is off by default.
also - are you aware any es_systems.cfg in /home/pi/.emulationstation will override the retropie-setup generated /etc/emulationstation/es_systems.cfg - you probably dont want that unless you are happy to maintain it manually.
This content on
https://retropie.org.uk/forum/topic/2359/emulators-not-displaying/17
Resolved the roms not appear.
I'm still dealing with being unable to set hotkeys on the controller.
Thank you for your help.