[phillc]

The length of time at full draw may affect you

Also if you get some one to video you indoors and then outdoors when you compare them, the positions are very different the angle of aim is much lower for indoors and you may just be in a position that causes the shoulder pain maybe your shoulders go out of alignment slightly when aiming lower .
I have just changed to compound and I notice the difference on a three spot face between the top and bottom.