I don't know. I'm almost convinced it's the cart itself. It is playable, so I went and got into the fortress part, where you control a guy and not the ship. Inside there, there were no glitches at all. It's only during the intro, the map, and the flight portion of the game where you see these glitches...
Anyone else own this cart that could maybe test it and see if similar results are happening? I've tried inserting it several ways. Air Fortress is the game.