I had basically the same issue. For me it was a permissions issue with the gamelist.xml that's automatically generated. Apr 14 v4.4 image.
I was getting an error that it couldn't save or write to /home/pi/.emulationstation/gamelists/snes/gamelist.xml when I quit emulationstation to the command line. Can't recall the actual message now.
Anyway you can check the current permissions by changing directories to /home/pi/.emulationstation/gamelists and run the command
ls -Rl
For most of mine, but not all, the gamelist.xml was owned by root for the owner and group. While others were set to pi for the owner and group.
To update the permissions of all the gamelists to pi for the owner and group, while still in /home/pi/.emulationstation/gamelists you can run this command
sudo find ./ -name 'gamelist.xml' -exec chown pi:pi {} ;
There are other ways to accomplish this, but this was what I'm comfortable with. Hopefully there's no typo, I'm going off of memory and I'm just finding all named gamelist.xml starting from the current directory then changing the owner and group to pi.
As far as how this happened, I don't know. I built my own gamelists from a windows machine with images and videos. Placed the gamelists in /opt/retropie/configs/all/emaulation/gamelists/ and they all had owners and groups of pi. Loaded the ComicBook theme. The images/videos are aren't in the same directory as the roms, they hang off of /home/pi/RetroPie/. These are the only things I've done from a stock image with the exception of setting up a keyboard and PS4 controller.
