Bumping this as I am having the same issue. Anyone come across a fix? it seems to only happen for Sega Mastersystem/genesis and lr-genesis-plus-gx, other systems and cores work fine.
For most people, this glitch is something that originates in RetroArch and needs a fix. A future release of RA will probably take care of it. In the meantime here is a workaround:
After the game starts and you see this happen, use (Hotkey + "B") to reset the ROM. It should come back with the whole screen visible.