I have recurring flares of rashes, joint pain, muscle aches, debilitating fatigue, dizziness. I have photosensitity and one episode of my WBC at 2.0 years back. My ANA is 6:40. I'm on plaquenil. Why are all my other antibodies neg for lupus?

Maybe SLE maybe not. Diagnosis of rheumatologic disease is generally based on symptoms with support from lab. Sounds like you have a rheumatologic disease and are being treated with a rheumatologic agent perhaps by a rheumatologist. They can explain your particular situation better, but suffice it to say tests are not always right and a single test does not generally make or break a diagnosis.
ANA 1:640? Concerning for lupus as is everything else you tell me, though the language is somewhat vague. Consider a visit with a second rheumatologist with whom you may have better rapport. Key to rheumatologic disease is the trusting relationship between physician and patient; perhaps the two of you simply did not hit it off, as has happened to me from time to time. Lupus is brutal, you deserve the best.
LUPUS. Are you under the care of a rheumatologist? They know what they are doing and will even tell you what kind of lupus you have, discoid or systemic? Pls ask your md.