Thanks for posting the shots. I'd guess:
http://www.merckmanuals.com/vet/poultry/omphalitis_navel_ill_%E2%80%9Cmushy_chick%E2%80%9D_disease_yolk_sac_infection/overview_of_omphalitis_in_poultry.html
Try an antibiotic that can be added to the water (Oxytetracycline for example). If you have an...