Sorry for the late response, I'm somewhat lost as to how this would have happened.
1. Any other mods? Multiplayer?
2. If you start the game, open the console and run /c game.print(game.player.surface) , do you get nauvis-factory-floor?
Either the factory gets created on a different surface than the game assumes, in which case the world should fail to start at all. Or it gets destroyed sometime later, which I can't seem to replicate.
