Confused about survival too.. Same things happens, enemy with lower initiative often outspeed me in last battles. Also a strange thing, I use the same main team in survial that normally use everywhere. It has less hp in survival, maybe less stats too.
One more thing: Its about sweep. I can complete whole survival with all ninja alive or barely sacrificing one if needed. It let me sweep till level 9 next day. But, if I change something in my team, remove/add someone, then it won't let me sweep any levels except first level and I have to manually play all of them.
If someone could explain these different facts about survival, tha'd be much appreciated. Why would we have less hp in survial? Why would our gears shift position?