Some dogs are just born more submissive.Doesn't mean anything happened to them or that something that did is still traumatizing them.I think if you can find a treat he likes reward him with it when he comes and give lots of rubs and petting he will warm up to you.As for your son I think its territorial and your son giving treats will help.Always move slower when approaching him while calling his name.(I will say while training since he is closer to you start with only you working with him, while building his trust).
I am not a trainer,but this is what I did when I took in my Sarah from a breeder that over bred her and cast her off sick to me.She was territorial toward everyone but me,skiddish and barked enough to wake the dead.She would definately try to bite and she would pee herself when called.
Everyone said she would never change the Dr's too.I just smiled and read lots of literature.She does not bark at all anymore even when my others were going crazy.She tries to bite no one.She is not afraid of anyone anymore.I can take her for walks and the peeing is a thing of the past.
So you see things can and will change you just have to find what they are responsive to.good luck
