You need to get them a heat lamp. They still aren't fully feathers and shouldn't be outside. The ducks didn't give the chicks the disease. You said you removed the ducks, did you re home them or something else? What brand of chick starter are you feeding? You said their crops never empty? That is concerning.
At night, can you take the food away until morning to assure they haven't eaten anything? Then feel their crops to see if its empty for full. If its full, its probably a crops issue. I have no experience with crop issues, so hopefully others can help.