Is there a 12 faction limit? That might explain why a 13th faction is not showing up.
Edit: I changed my player template ini and saved that back to the original BIG file. I removed the superweapon general. IT NO LONGER EXISTS, but run the game and it runs fine with the deleted general.
WWWWWW TTTTT FFFFF?!?!?! Is he a ghost or zombie? He is not in the player template anywhere.