Diagnosing lupus can be very elusive and can take months or even years to get confirming labs. As others have stated you can have lupus but tests can be negative. Welcome to the world of autoimmune disease. Until your labs and symptoms are more conclusive your doctor can't be sure. You should ask what makes him think you have something else...specifically what.
MCTD (SLE Lupus, polymyositis, scleroderma). Diagnosed 2005. Kidney, liver, GI tract, dysphagia, raynauds, barretts esophagus, quadriplegic in 2005. Recovered and now active in downhill skiing, golf, hiking. Meds: amlodipine, benezapril, omeprazole, potassium, folic acid, vitamins, maxide.
Remain Optimistic and you can overcome.