Did you change settings to get it to work with (or looking better with) the PS2? It’s possible when changing settings, you have now made the output from the genesis incompatible with the TV.
If you’ve got things looking good with the PS2, I suggest saving that as a profile. The go to Settings Opt -> Reset Settings.
Now you can test, and see if you’re back in business at default settings.
If you want to take it further from there, then use FBX’s optimizations to dial in the OSSC for the Genesis: http://www.firebrandx.com/osscprofiles.html
Assuming (hopefully) that gets you back in business and even looking better than before, then save that as a profile (or one for 352 line games and one for 320 line games).