You may be short drawing the bow and your arrow is overspined. I hurt my shoulder during the season last year and had the same issue.
Yes, either short drawing or collapsing at the release. When you bareshaft stretch out the distance as much as you can and shoot several times only paying attention to the average. With a bareshaft any form inconsistencies will show greatly so it's better to take a reading from 2 dozen shots than 3 or 4. When I am shooting perfectly,I have grouped bareshafts perfectly in with my 45 yard feathered arrow group. Pluck one though and you will completely miss the backstop.
