Sounds like you are answering your own questions. Shoulder injuries are often slow, insidious beasts that eventually become painfull overnight.

Watch anyone doing the cross and you see the imbalance required in fact to do the exercise for it is not a "Normal Movement". You are going to need a balance between internal and external shoulder rotations as well as direct and indirect scapular depressors such as lats, serratus and lower/middle trapezius. Rhomboids are also impt when the arms are out at 90 degrees.

Get a friend to hang partially supported in the position and take a good look from all sides to see what muscles are in play. A fatigue in any of them will give you various impingements. Interestingly if you can do the cross but not a vertical press into a handstand then maybe you have some nerve issues already and you shouldn't be training the cross at this time. (to much to soon)