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Most 'prey' animals are naturally afraid of overhead movement/contact because they get attacked from above. They're also naturally terrified of being picked up, because in the wild being picked up meant you were caught and about to be eaten, so it needs to be avoided at all costs!
Try coming from below and stroking their breast or side of the neck rather than their backs or from above/behind.
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Absolutely, when I put my hand in to "mess with them," they always respond better to having my hand under their eye level. I scratch my babies and even adults on the lower breast.........coming from below them. Even the most skittish birds are less frightened using this method.
One other thing I've noticed is, certain lines can be more flighty and fearful than others. Unfortunately, I had some chicks in the beginning that never did settle down completely. They're not here any longer.
Nancy