I would guess it might be the pine bedding. I raised 6 Rouens for a month in a large flight cage in the house on paper towels over newspapers then when they outgrew that and got messier I moved them to a pen in the barn w/pine shavings. I think some started to eat the shavings as I lost one. I had been cutting greens for them and tossing them on the floor (as I did in the flight cage), but with the addition of the pine bedding, think they were eating that as well. I did leave the bedding there but put the greens on a tray so it didn't mix in with the bedding. They are 3 months old now and getting adult coloring and swimming in our outside pond - all very healthy. They figure out not to eat the bedding as they get older but for tiny babies I wouldn't use it in the future until they are a bigger size. Good luck.
Yeah, most people recommend not using pine shavings because they eat them, but I know with small animals like hamsters or rats that it can cause respiratory problems. Aspen shavings are recommended over pine and ESPECIALLY CEDAR (worst of all) because it doesn't have any aromatic oils to irritate the lungs.
Of course, I use pine one the babies are old enough to ignore it for the most part.
I'm gonna agree with Wifezilla and say these things just happen sometimes. We always put either paper towels over the pine shavings or a rubbermaid shelf liner (it has holes in it) to keep them from eating the pine shavings at least in the first few days. I might try a different container, but some little fuzzybutts just aren't as strong as others. Good luck with the rest! And post pics when you can.
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I order from a hatchery on a weekly basis. It takes two days to arrive at my post office. Due to the length of time that it takes, not all survive the trip.
Thanks for all your replies. I cleaned everything and tried covering up the pine pellets with newspaper. That was a horrible mess so I gave up on it. We haven't lost any more ducklings since day 2 and the others have more than doubled in size. My fingers are crossed but I think we're out of the woods. This message board is so helpful!