HDMI or composite ?
What is your default video resolution ?
If you have the latest retropie-setup script, please try
sudo ./retropie_packages.sh runcommand
sudo ./retropie_packages.sh stella configure
and try again. if you get a black screen then go to launch it, but press x or m on the keyboard a few time before it loads and you should get a video output settings. you could try setting it to your native screen resolution. You should probably then do
sudo ./retropie_packages.sh dispmanx
and turn on dispmanx sdl for this emulator. it should then nicely scale up to your native resolution.