Some kind of predator, a small one, is getting in and eating your chicks.... that is one hideous looking rat (shrew?) in the picture...that thing would get shot on sight.... LOL.
I read you are not liking the rat poison.... I understand about the smell, but you will never make a dent in that rat population without a concerted poisoning program. Rat poison for a start... you need to knock down that rat population. I like to use a bait station so no one else gets poisoned (except that hideous Jimmy Durante looking rat).... It could be that. It could be alot of things. Do you have Mongoose there in the PI? Any small predator could be doing it, I would secure those chicks in a separate more closely held container until you get a better fix to your perimeter. You have to close it in securely against all threats, airborne, crawling, large and small... someone said hardware cloth... If you already have the fence, maybe some chicken wire would be enough.... Smaller openings is what you need.
Whatever the killer, it is nocturnal and small as evidenced by it selecting your chicks first. It is likely coming in and out through the fencing. And it is going to keep coming back til they are all gone and then it might even start on the bigger chickens. Good luck with this one. (It is not your chickens that are doing that.),.