I found this in a book written by a dog trainer, but I don't know that this is your problem, either...
Hand-shyness...a hand-shy dog must be carefully desensitized until it learns to enjoy, rather than fear, hand contact.
When the dog is calm and relaxed, slowly put your hand underneath its chin and stroke it very gently, as you talk to it in a soothing way. Repeat this day after day. When the dog is completely comfortable as you do this, very graduallly move your hand until you can stroke it all over.
Sometimes a Food Reward will help you get close to a very hand-shy dog. Hold a treat out in your hand and, when the dog comes to get it, stroke the animal gently underneath the chin.
It may take a lot of time and patience to desensitize an extremely hand-shy dog.