Why are all my childs blood tests neg but they say he has ra?

My 13 yr old son was diagnosed with JIA in June but they say he probably had it his whole life . It has become a nightmare, every test just shows, more damage, including demineralization in his bones, erosion and loss of growth in his jaw, uneven bone growth, arthritis in his c-spine. He is currently getting pt and ot and is on methotrexate and humira. He also wears hand splints at night to prevent worsening of his loss of rom in his wrists. I have an endoscopy scheduled for wednesday to r/o any gi problems. I've also taken him to an allergist to r/o any allergies. So far all his blood tests are negative for inflammation, RA and allergies. Do you think he could have an underlying neurological problem that could be causing the arthritis.?