First, I am very sorry for the loss of your feathered friends. It is very hard to lose one and not have an obvious reason why it happened: It can be downright scary.
You need to start carefully looking at everything from their food to their housing. You may find the answer through process of elimination. Take away the first suspicious thing, wait, then try another if you are still having issues.
What are they sleeping on bedding wise? Waterfowl seem to be much more sensitive to environmental toxins than chickens.
I have gotten a moldy bale of straw for bedding: It looked and smelled fine, but I use gloves so didn't feel the powdery stuff on it. I used it as bedding in my goose house and chickens nesting boxes. Within 48 hours I had two dead geese and a third sick one. It was when I changed the straw in the hospital cage to some of the good horse hay that the third goose almost immediately began to improve. The light bulb went on and I checked the straw and found the mold. I cleaned it all out of all the housing, then thoroughly cleaned all the houses, bleached the floors, and put in the horse hay: No more issues.
Because they love to dig with their bills, is their any chance they came upon food that had been on the floor and become buried and spoiled?
Are they allowed to free range during the day? If so, are their any plants the ducks seem to be eating that the chickens don't bother with?
Good luck and I hope you find the cause very soon.
