I know this sounds backwards. It is my first day paddling a Greenland paddle. And after a few minutes my right shoulder hurts. This never happened using a Euro blade and I never have any shoulder or other joint pain after paddling. I was using a canted forward stroke and what seemed like good torso rotation on very flat water. I did notice how the paddle was trying to pull downward which I had expected. Perhaps I was resisting that pull too much? Kayak is a Manitou 14 (14’3" x 24"). Otherwise I had good results for a first try.
You are using the muscles in a different way, even if subtle. It may take them a while to adapt.