First this sounded like a strain of your upper rhomboids. However, the failure to improve with rest and PT, would make that unlikely. There may have been an occult fracture of your scapula, but again rest and time would have resolved your symptoms.
I would suggest two possibilities. First, a herniated cervical disc with cervical radiculopathy, second, suprascapular nerve entrapment. MRI of your Cervical spine and EMG's might be useful, if they haven't already been done.