I too have suffered from shoulder pain for the last few years. I first noticed it after trying to prune an apple tree in my garden.
A couple of years ago it got so bad I had to consult my GP. She sent me to a physiotherapist at the local hospital. He was a young lad who was still training - but because of this he was very conscientious. At first he thought that I had arthritis but, after fairly exhaustive testing decided that I had inflamed tendons. He then treated these with a combination of massage and ultra-sound (I think - can't remember exactly). After a couple of sessions the pain went away.

Back in November of 2006 the pain came back with a vengeance. This time lots of joints (knees, fingers, toes as well as shoulders) ached like fury. After a few days only the shoulder pain remained and I treated that myself with one of those deep heat gel pads. I think that this last episode was down to some sort of 'flu-like virus which attacked all the weak joints in my body (I know where they are now!).