The only times my shoulders ever hurt were when I didn't have my pack adjusted properly. Then the pain would be surprising... I didn't use my sternum strap, or have it tight enough when I did use it. That caused the shoulder straps to ride out and onto the knob of bone on top of my shoulders, in addition to throwing off the weight distribution. I ended up carrying too much weight on the shoulders in the wrong place and couldn't get it figured out. Finally I tightened up the sternum strap and it all fell into place.

Hope it helps.