I had a similar problem….my monitor (1366 × 768) was jagged on the screen. So I manually forced the resolution on the emulationstation.
Entre no bash
1 execute : batocera-resolution listModes
veja as resoluções disponiveis.
2- execute : cd /
3- execute : cd /boot
4- execute: mount -o remount,rw /boot
5- execute: nano batocera-boot.conf
6- add es.resolution= “put Ur resolution”
7- save de file
8- execute: batocera-save-overlay