K.H.
My daughter is about the same age and we occasssionally have those set backs and I have also wondered about nightmares. I am not sure, but I know some of the crying seems so horrible, I feel like a heal if I don't do something, then feel like I've been 'had' when I realize a pattern is forming. Yes, I think they can learn to manipulate at that age (who can blame them, right?). My recent tactic has been setting in the rocking chair in her room, usually listening to my ipod so she knows I am there, but I am not reinforcing that midnight cries get you a big reward.
I feel your pain, momma!!! Hang in there.