tl;dr
Type this in after you login as user 'pi'.
sed -i 's/runcommand.sh 1/runcommand.sh 2/' ~/.emulationstation/es_system.cfg
EmulationStation
Couldn't find any solution online for this specific problem, so writing this down.
Running emulators in EmulationStation is a bit different from running the emulator binary directly from the prompt. runcommand.sh script sets up random stuff that you don't necessarily need, especially if you are using a modern day TV and Raspberry Pi connected with an HDMI cable.
The first argument to runcommand.sh specifies what you want to do with the output. "1" sets it as "run in VGA mode or something even if you are using HDMI or DVI". Not sure under which circumstance it makes sense to use such setting. "2" says "just use the current setting." SGTM.
The command above rewrites runcommand.sh 1 to runcommand.sh 2.
