I just reread and saw the detail about the nesting box. Yikes. Let's tag the experts; they may not be available until morning but they'll have better, experience based input!
@ChickenCanoe @Eggcessive @Wyorp Rock @aart @DobieLover ,
I'm very sorry I don't have better answers but we'll do...
Oh honey, I do not know! You're right, it doesn't present like standard coccidiosis but I'm not sure what IT is! Any chance your girls caught and ate a mouse or something from the roost?
Short of having the droppings tested by a vet I think just putting down fresh paper and keeping an eye out...