maybe your serratus muscles are weak. The serratus rotates the scapulae so that the arms can be extended overhead.
Try this: pull your shoulder blades together and down, like everyone recommends you do when you bench press. Now raise your arms. Feels funny, doesn't it?
Your traps are probably compensating for the serratus' inability to rotate the scapulae against a load. Since the serratus can't adequately pull the bottoms of the scapulae outward, the traps compensate by pulling the tops of scapulae inward.
Besides strengthening the serratus, try doing all shoulder presses in the bottom-half of the range of motion only.