Aero,
There's a bunch of reasons for shoulder problems. There is your shooting form (90 degrees to the target and upright stance VS open stance with an unlocked elbow etc.) there is the matter of draw weight (you could try shooting a bow with as little as 5# less and see if the soreness subsides) then there is the matter of your draw length...if you are in the habit of extending the bow arm as far as possible to gain length you can alter the natural orientation of the joint.
If I had that problem my first thing would be to lighten my draw weight maybe 10 pounds (some Ibuprofen for inflamation) and shoot a fair amount to see if that helps.....if not ya may want to take a close look at how you actually hold the bow while you are shooting........I'm one of those old guys you been listening to lately, I didn't much like having to go from my old 60-65 pounders to 50-55 but the pain left when I did that, and the accuracy improved because I was no where near as sore.
rich