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You could be experiencing some impingement, which is basically just soft tissue getting pinched up in the joint. In this case, let’s use the overhead position as an example, it’s probably aspects of the shoulder joint capsule getting stuck in the subacromial space (beneath that pony point on the outside of your shoulder). This problem can occur easily overhead if the shoulder blade isn’t moving correctly along with your arm. The shoulder joint itself only has a limited capacity to accommodate raising your arm up; you’re able to reach overhead because your shoulder blade rotates to point the shoulder socket upwards.
If this is the case, an easy fix that you might not have gone after yet is clearing soft tissues restrictions around the shoulder blade. Trace the inside and bottom angle of that sucker with your lacrosse ball, give it some room to breathe, and you might just find that pain disappear.
From a motor control perspective, sometimes I find that people go overboard in their efforts to stabilize the shoulder overhead by trying to hold the whole shoulder girdle down and back. While you want to maintain some space between your shoulders and your ears, you still need to allow the shoulder blade to rotate (and elevate, a bit).
I hope that offers some insight! If you’ve already done this, we’ll go back to the drawing board.