Some chickens don't like to be touched........
Did you see that old B&W Boris Karloff movie "The mummy" -- it has a line in it -- "I don't like to be touched, an Eastern custom, I fear" or something like that.
You didn't say which breed you have, but some more than others don't integrate REALLY well with humans, they want to remain in the bird-world. Having them eat out of your hand is one thing, actually picking them up and holding them beyond the normal inspections for mites or other treatments could be just more than some breeds will ever enjoy having.. In your case, especially if you raised them, they would be 'imprinted' on you.
Part of the 'bonding' with chickens too, is the degree of automation. The more automation, the less they really 'need' humans.
Hope that you can coax them to be more pet-like and friendly if that is your aim, but also remember some birds just don't like being cuddled.