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Are those the only vents on the incubator? If so, I'd consider adding a few more small holes to the sides and bottom.

Is your incubator still or circulated air? Do any of your thermometers give you a high/low reading (so you know for sure there wasn't a dip or spike)? If your air cells looked good and the ducklings didn't appear real wet inside (which I assume they didn't, since you didn't mention it), I'm...