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I just shot off an Email to someone who contacted me about how to deal with a shy rooster.  It's pretty long, probably too long to post here, but I'd be more than willing to Email it to you ( or is there a Private Messaging system here in BYC? ).  Perhaps my next post should be about socializing and handling shy and skittish chickens!  I think the biggest key element, though, would be to NOT allow yourself to bend to "feeling bad" about them.  Their hardy and they can handle a whole lot more than we give them credit for.  If you have EVER picked up your birds, even as chicks, they struggled a little, and you immediately dropped them then they have learned and been reinforced that being held is a BAD thing.  They would have learned to abhor being held even more if ever once you cooed and cried over the situation.  "Oh, you poor thing!  I'm so sorry!!"  I tell my rooster I'm sorry if I accidentally clock him ( like I did with my laptop cord just a few minutes ago ), but only if he's calm.  The only physical attention I give in such a situation is a quick check to make sure there is no injury.
When it comes to being handled, socializing chickens, and desensitising them to people, I force them to put up with a lot.  The rooster I tamed from a human aggressive rooster to sitting at the foot of my bed began with going out at night and grabbing him from the coop, where when he flailed I would hold him upside-down, holding his legs near his belly, and my whole hand grasping the back of his neck to keep him from pecking me and also to limit his options for flailing.  When an animal panics, they have two options: Move or relax.  Take away the option of movement, and they're forced to relax - but be careful not to OVER-restrain them, too!  As for chickens, just the act of being upside-down is calming for them.  When he would relax ( and that's not just not flailing, that's when I felt the tension of the body release ), I would flip him back rightside-up.  If he flailed more at the movement, it was back to upside-down until he relaxed, then rightside-up and so forth.  When he calmed down, I would adjust my grip to be hugging him against my body where I would bring him inside to watch movies with me on my lap.  Point being, though, that I showed him a situation in which he perceived potential danger because he had not grown to trust humans for good reason, but I moved past this by showing him that if he were to relax, good things happened to him.  After about a week I could easily approach him without him running away - but my house mates couldn't.
On a larger scale, this could be a tricky way to progress... however, if you manage to get one chicken to trust you, it can often make things breezier with the others.  You mentioned using treats... try making it so they can ONLY get their treat if they take it from your hand.  Then get them so they can only get their treat if they take it from your hand while your other hand is palm-up facing them.  Then if your hand is moving.  Then if you're touching them ( when using this method, I start with touching the breast, work my way to their head, and down their back ).  Then if you're stroking them.  Then if you're holding them.  I have had success working up this way, but again, I was treating only a single chicken.
Also note that even if you DID inadvertently train them to not like being held, it is NOT irreversible - that just means it'll take some time and dedication on your part to convey a different message after all this time.  You also need to work hard to be very, very consistent with your message.  You can NOT give them mixed messages and expect positive results from them.  When dealing with unwanted behaviour ( skittishness, aggression, etc. ) be quiet and stern but gentle.  Always have them know that there are RULES and you expect them to be followed at all times regardless of your presence.  However, when they are behaving in ways that you desire, crank out all of the cooing, praise, treats, petting, and anything else you want to give them.  You should be seen as an equal amount of discipline and justice as well as affection and fun.  Lastly, discipline and punishment are two VERY different things.  Discipline is disagreeing with a behaviour in a manner that the animal understands ( dominating behaviours such as the neck-pinch and push down ), whereas punishment is anger and aggression that the animal doesn't understand at all ( hitting, kicking, yelling, etc. ).  NEVER punish your animal, but don't ever hesitate to discipline.  Animals discipline each other all the time.  It's natural and it's understood - the only thing that might confuse them is why YOU suddenly start doing it!  But once they get over that initial confusion, they'll start to listen.
Anyway, that Email I mentioned above goes into greater detail in different approaches to dealing with skittish chickens, and my varying degrees of success with each one.  Send me an Email or Private Message or something if interested.
Lastly, I am SO SORRY that I seemed to have unintentionally hijacked your thread, Louie!!  I just wanted to help people help their animals!!