Me too. Fixed it by fixing my style.
There's a couple of good videos that can help:
www.seabreeze.com.au/Articles/Stand%20Up%20Paddle/How-To-Paddle-your-Stand-Up-Paddle-Board_2919938.aspxChanged my paddling completely from a pulling back motion to a pushing forward .. less stress on shoulder, stronger stroke .. and no shoulder pain!
Can also be too long a paddle .. some suggest you should be pushing from the chin forward .. any higher & stresses the shoulder?
Hope it helps ... dud shoulders are the worst.