This is a major problem in Berners and there are several national health efforts to breed out shyness in the breed. Until then, it continues. Most shy Berners are so by lineage and you can improve it some, but will not eliminate it. Shy dogs should never be bred, so talk to your breeder for assistance and information on the parents and their shyness.
For many Berners, they are such a sensitive breed that they can become shy through experience and the fear imprint periods. If something traumatic (and it can be really small in our view) occurred during one of the fear periods, a Berner will never forget. Berners commonly generalize their fears, so if a man scared him during a fear imprint period, he could eventually start generalizing to all men or all strangers.
What you are describing is serious shyness with a high flight instinct - I have a rescue here that I am fostering and rehabilitating until we can place him and he has the same fearful behaviors. I have been working with him for 6 months to counter condition carefully and he has come a long way. I am working on a second Berner, a female right now with a less significant shyness issue but she will likely take just as long. It is critical not to take them out into heavy public places and allow strangers to approach with outreaching hands - every time this happens, you reinforce the fear and make it harder to correct. So it is important not to "practice" the fear so to speak. Never try to force him to endure the scary strangers and put him in a fleeing position - this is called flooding and is very detrimental to long term recovery.
Understand the patterns and triggers - is it men? small children? all strangers? strangers with sunglasses? etc. so you know what to avoid. Don't allow the two of you to get blindsided either. For my foster, it is small children (he is now over men) and I step in front and put my hand up to politely stop any and all children from approaching him. I explain that he is scared and ask them to all stay still, avoid eye contact, and hand them treats. They stand at whatever distance is necessary for the dog's comfort. They throw the treats on the ground in front of the dog. If the dog will take the treats, then they can start throwing them closer to themselves so the dog advances a little. If the dog is willing to approach, I let them hand the treat out in their hand.
I strongly encourage you to purchase Patricia McConnell's "The Cautious Canine" for a solid counter conditioning program and guidance to overcome this:
http://www.patriciamcconnell.com/books-retail.phpShe walks you through everything including exercises as home you can do with a stranger coming to your door etc. as well as outline the pace to work so you don't push the dog too fast and venture out into the scary situations. Her program has a phenomenal success rate.
