As you already know, the anatomy and biomechanics of the scapula are complex. With 17 muscles that attach to the scapula and the spinal accessory nerve and long thoracic nerves, there can be any number of different reasons why scapular winging might develop.
Causes of scapular winging are broken down into two groups: primary and secondary. Primary scapular winging occurs when one of the main muscles that hold the scapula steady stops working as it should. Make sure you thoroughly evaluate the trapezius, rhomboids, levator scapulae, and serratus anterior muscles for any impairments in strength, endurance, or motor control.
Injury to the nerve controlling scapular muscles is one cause of primary scapular winging. Athletes are at greatest risk for nerve paralysis causing primary scapular winging. Whether an athlete, homemaker, industrial worker or other individual anyone who suffers a fall, collision, or repetitive motion could develop this problem.
Secondary scapular winging is the result of a problem somewhere else in the shoulder complex. That other problem could be a rotator cuff tear, shoulder bursitis, shoulder dislocation, or a frozen shoulder. Part of your examination will be directed toward screening the shoulder joint as a potential source of the problem.
Osteochondroma (bone tumors) can also cause secondary scapular winging. With osteochondromas, there is usually a “clunk” that can be felt and heard as the arm moves away from the side just as you described.
An X-ray or other more advanced imaging would be needed to identify osteochondroma as a potential cause. If you have conducted a thorough evaluation and cannot identify the cause, it may be time to refer to a specialist for a medical diagnosis. There could be something else going on that cannot be easily determined without lab work or imaging studies.