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Probably she doesn't think he is dominant of her even though (or maybe because) she grew up with him. If she lets the other rooster mate then the other is dominant to her.
Oh, you say your boy only has one girl? Well - that might be the other problem - Silkie boys can usually handle 4-5 girls - and with only one he wants to make her 4-5 times more than she wants to be mated.. so that may be why she is running. When you get a bigger flock hopefully that will cure the problem.
It could also be he hasn't figured it out yet too. My one Partridge boy I got at over a year old - well he was being too nice and none of the hens would squat for him - and so none of the eggs were fertile. When I moved them into a cage side-by-side with a much more dominant roo I think the Partridge boy got some lessons from watching him about being boss and now I have seen him mate the Partridge Hen and the Buff hen (that is until she decided to go broody.. again
) I am working on getting him more girls too.