Repeatable shoulder clunking after two years from slap repair and bicep tenodesis

Problem: Clunking sensation that is repeatable when arm is directly up and out front, such as doing a push up, and hand is locked into ground, and shoulders are retracted, putting gleno head in posterior part of the shoulder, while internally and externally rotating. Does not occur when arm is pushed into ground with shoulders blades untracted, almost like a punch, while internally and externally rotating. Only when shoulder is back. Also occurs when doing following kettlebell exercise: Soldier Athlete: Supine Kettlebell Internal & External Rotation - YouTube

After I showed my physiotherapist he pushed his finger up and deep into the joint, by armpit area, towards my ear, and asked me to try and internally/externally rotate to repeat the sound and the clunking sensation went away. Comes back when he lets go. Physiotherapist is unsure what is going on.

What is the cause of this and how do I fix it?