I can't tell you what it is, but my best advice is to stay away from exercises that aggravate you. Stopping skull crushers won't kill you. Personally I loved the exercise, but they eventually hammered my elbows; so much I thought I had really injured them. I worked around it...and I'm now fine.
On another note, 10 months ago I had major shoulder surgery for a 100% tear of my right rotator cuff and to remove a big chunk of my labrum that was floating around. It was 6 months of hell, but I'm ready to get lifting again. I have totalled International Elite at 242 in the USAPL, so I know what its like to lift heavy. Never had ANY shoulder problems until I was rear ended in my truck by a 1 ton van going 50 mph. Right hand on steering wheel...straight...and it popped. My whole point...........you can prevent most (not all) future problems by not aggravating the joint with certain exercises.