I think I figured out what spooked the babies the other day.
We have a big flock of wild turkeys that crosses through here every few days- probably about 20-25 total counting the babies they have.
Today I was cleaning the chickens' pen and heard some weird rustling on the hill behind me, turned around and the turkey flock was hanging out right there. I think we both surprised each other, and the turkeys took off flying up into the trees (those things can fly HIGH and FAR- who knew?!). The babies took one look at them and bolted for the coop, refusing to come out.