I have the same thing on my shins, massive calcium deposits and had stress fractures.
I got it from long distance running and had to give up on the doctors orders, although I had a few serious operations and major virus in my leg when I was a child, so it was a different case.
What the physio is doing is trying to break down the calcium deposit and scar tissue by deep tissue massage. Its quite normal.
You should also be getting Infra Red therapy, and Sonar therapy (if thats the correct name) around the shoulder joint and bicep tendons.
I think Arnica is also recommended for helping to disperse the calcium deposit and help with the pain. I would try to find an accupuncturist, seems to work wonders.
The physio should also be checking the alignment of your spine and traps etc. to ensure nothing is out of sync, as this is frequently how these problems occur.