I'm so sorry this has happened to you. I'm thinking it may have been the shot, or perhaps something happened while he was boarded there, a fight with another dog, or some type of accident? The problem is either way, the hospital might be liable, and I'm not sure they are willing to give you the correct diagnosis because of this, there just might be a conflict of interest.
I would find another vet not associated with the hospital. Sending prayers your way, I hope you get to the bottom of this.