Pyramid is roughly halfway through the game. I got hit with the bug and only had 3 people on the first party no matter what configuration I made. That didn't stop me. I beat that half of the dungeon with 3 people and just moved on past it. Don't know what causes it, it didn't happen to my friend when he played. I reloaded twice and it did it to me both times. Can't remember which version I was playing on at the time. Just went "Challenge Accepted" and smashed it.