Hi Ann Marie,
So what happened with the puppy? Did you take him back? I've seen dogs adapt amazingly well to deformities, and the one you describe does not sound all that debilitating. I can see where a small ankle bone could be a problem for a large dog, but I would guess with exercise early on aimed at keeping his leg muscles strong and keeping the dog on the lean side, this shouldn't pose any great long term problem. I guess for me, I would be more devastated to hear that my puppy has severe hip dysplasia. With that, you are guaranteed to have to spend serious $$ on surgeries and care.
In the end, it comes down to your own personal choice. Surely, it is better to return the puppy to the breeder now while he is young and can be more easily rehomed. Like the previous poster said, talk with the breeder and get second and third opinions from qualifyed vets before making the ultimate decision. I know it must be breaking your heart, as he had been with you for several weeks and I am sure you are already in love with the little one. There is a yahoo email group for people with Berners that is an amazing resource with over 1600 members (owners, breeders, and vets). I bet if you post this issue to the group you will get very good information about this particular deformity.
Let us know what happened!
Lori