It might be an idea to invest in Carol Price's book "Understanding the Border Collie" too :)
I get the idea from your post that you have got men to initiate contact with the pup (ie give him treats) ... this is not a bad thing as such, but for this to work the initial move has to really come from the pup, otherwise they are "forcing" themselves on him. When they then retreat due to his lack of co-ooperation, this is teaching him that barking works to make some scarey men go away!!!

I would suggest one thing you could do is to make life wonderful for him when men are nearby or pass by - treats, games, etc. For treats you could use liver or chicken, something really tasty. This is a form of conditioning which can get a dog associating the very "presence" of a person or thing, with enjoyment.
I agree it is also an excellent idea to tell him what you do want him to do, as this takes the onus from the pup to you ie, he can trust you to be his leader and keep him safe.
When men come around, you could also try getting them to totally ignore him (keep him in another room maybe so he isn't too reactive) and then get them to drop a few titbits on the floor but with NO effort from them to make contact with him. Eventually again, he should realise men bring tasty things and after some time make some sort of overture, even one step towards the men...but beware of going too fast.
Socialise him as much as possible but don't let men push themselves on him or ven try to get him to accept them, make sure uou remain in control of the situation ;)
Lindsay
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