i haven't watched for a while, but my interpretation is that the only known way of winning the Alice Game is for one Rozen Maiden to kill/defeat the others. Shinku beat Hina, but was generous to provide her with some life force and not kill her. This was only a temporary solution, and she wound up dying anyways.
Boku was killed by Suigintou. She, like Shinku was a real Rozen Maiden.
However, all the others were killed by Bara. As a fake, her kills didn't count in the Alice game, so when the Rozen Maidens came to life, only those who lost legitimately remained dead.
Think of it as a basketball game (Alice Game.) If some guy in the audience (Bara) randomly ran out to the court, grabbed the ball, and threw it in a hoop, does that mean either team gains a point, even if this random guy managed to score one according to the rules of the game?
No, because he is not a player, so his actions don't count.