I start to believe that it is a hardware timing issue with the cartridge (at least my copy which looks and feels super high quality btw). When power comes on the cartridge is still initializing/booting itself when the Mega Drive gives it control too soon. This explains why game genie in between works, because then the metal gear cart gets power and can initialize itself before it is given control to really boot.
The metal gear cartridge seems too slow on startup to be ready.