I notice my TV switches from HD to VGA input when a ROM is loaded. Does your TV automatically switch it’s settings when it detects an input that changes?
Looking at that file settings, have you tried setting your video resolution to the native for your TV to minimize the change?
# Fullscreen resolution. Resolution of 0 uses the resolution of the desktop.
#video_fullscreen_x = 1366
#video_fullscreen_y = 768
# Start in fullscreen. Can be changed at runtime.
# video_fullscreen = true
I’d try setting your fullscreen settings to your TV native (The one Emulation Station runs in) and fullscreen to true. Remove the # mark prior to the setting.
Just an idea, I have no expertise in this.