Yes, a rat will carry chicks off. If you're using chicken wire, a weasel can also get in and kill your entire flock, including adults. They'll kill a whole flock in one night just for fun. Sorry you've had such a rough time of it.
I think that's poo in the shell...
I agree with above. Just like with human birth, the first poo can happen at any time, even before birth, which is a possible medical emergency due to the infant drawing the meconium into the lungs. It can happen during or many hours after the after birth...
Bubbles, you gotta build a bator. Great winter project! Amy, congrats on the hatch! Hope you continue your thread re: integration of bator chicks with broody chicks.