It's an interesting thought about the rat and/or snake. There was always one other chciken hanging out near the nesting box, so I wondered if he got the first chick. So when I saw the second coming through, I moved Mama and the clutch to the "nursery," a closed off space at the back of the coop where my other 2 hens with chicks are. They each have a nest in an cat carrier (door open), so it'd be pretty tough for a snake to get at them. Plus, the other chciks, including the one of hers I had moved under another hen, are all hale and hearty.
This morning, another peep had hatched. I lifted her off her eggs and saw the peep, put her back down with the chick not under her, and she STARTED PECKING THE CHICK'S HEAD! I may be convicting her on less than concrete evidence, but I moved this peep under another mama, too.