My knees hurt and stiff when sitting to long but only last 10 min, fatigue , have pos ana but neg rf, family history autoimmune disease so what wrong?

Check with your: Rheumatologist. It probably is early RA or one of the other autoimmune disorders, affecting your knees. The rheumatologist will be able to DX it for you and start treatment. Good luck.

Further evaluation: You may have an inflammatory arthritis associated with an autoimmune disease. I suggest continuing an evaluation with your rheumatologist.