I just started playing DG last year, shortly after having rotator cuff surgery. At the time, all I could throw was forehand, due to my severely limited range of motion (I couldn't even reach across to buckle my seat belt). At first it would get my shoulder pretty sore, and almost reached the point I didn't think I would ever be able to play. First things first, take the time needed to let your shoulder heal. What I learned to do in the beginning, was to stretch good before a round, and, stretch again before teeing off at each hole. I carried roll on Icy Hot to apply immediately after each round, and, when I got back home, I would ice the shoulder down for a half hour or so.
Now, for the issue of what's causing the pain. Technique. Once I learned to quit putting so much power into my throws, and concentrate on throwing properly, my problems went away. I use less arm now, and more body to gain arm speed. Concentrate on more spin/snap, using your wrist, and grip. And make sure to follow through with your throw. This was my biggest improvement as far as pain goes, because before, as soon as I released the disc, I would stop my arm (as if I were whipping a towel).
David