I've had JRA since age 5, and I've had 5 total joint replacements in the past 30 years including both shoulders.  I've developed a quite a high tolerance for pain, so I truly didn't notice the signs when my shoulders began to be attacked by my faulty immune system.  Looking back though---it was obvious what was happening.  Something else--- people with RA learn to compensate for pain and stiffness by leaning to another side, putting more weight on another joint, and other things that we are often not even aware we are doing.  When my shoulders first got bad, I adjusted my behaviors considerably (For example:  I sat up with a book on my lap to read rather than laying down and holding a book up or laying on my stomach and proping myself up on my elbows. I leaned over to brush and shampoo my hair.  I fastened my bra in the front and twisted it around).  It wasn't until I had total frozen shoulders that I was forced to deal with the problem with intensive physical therapy and eventually with surgery.  There was pain in my neck and at the base of my head, but also in the upper back/shoulder area.  I also had considerably painful bursitis in my shoulder.  Don't wait for physical therapy because total frozen shoulders is incredibly debilitating.  AND once you lose your cartilage, don't wait too long for surgery because the worse your muscles and range of motion get, the harder post-op recovery and therapy will become.  Talk to your Rheumatologist and get X-rays because it is always better to know than to worry.  Good luck.