Only beasts will respond to rally all flag. I've tried using control groups, dropping minions on flags, using all possible flags, slapping them silly (out of frustration), everything I could think of. I've finished the game and am running through a second time to get the achievements. It didn't do this the first time through, but as I go to replay the level without restarting campaign progress I'm experiencing this issue. Might try resetting campaign progress if worst comes to worst.
Customer support service by UserEcho