My son had some elbow sorness fall of 2009. Went to a doctor to check it out. He prescribed PT and they discovered the same thing you are talking about. His pitching shoulder was a little weaker than the other. Did the PT they prescribed and he has been doing bands and light dumbells to keep his shoulder strong ever since then. He has not had shoulder or elbow pain since then.
Like BOF said, follow the instructions of the PT guys. I could be wrong, but I think when your shoulder weakens, it interupts the kinetic chain of throwing. The arm tries to compensate for it and the elbow suffers as a result. There are others here far more knowledgable than me, so they can correct me if I'm wrong. Just wanted to let you know, we had been through something similar.