She only had two babies.
I'm pretty sure she didn't have more and eat them. She wasn't very big (hence why I thought she wasn't as far along).
The other two mice are plumping up nicely. Cupcake is about to burst! All three females are currently taking care of the one baby left (I fed the other off). I'm not sure if I want to let Cookie raise it to weaning age or if I just want to feed it off and put her back in with the male.