You are right about your gluten free diet skewing the test for antibodies to gluten. It will. However, the gene markers will not be affected by diet. I recently tested positive with both genes, and a low positive antibody test. Along with my signs and symptoms, it was enough to diagnose celiac. If you do not have either gene for celiac, it is very unlikely that is your problem. I have read that you can have a wheat sensitivity that is not celiac, though. At any rate - if you have both genes, the liklihood that you either already have celiac or will develop it at some point is very high (it can be triggered by stress, infection, trauma, etc.) Knowing you have both genes can be valuable even if you have no symptoms at present, so you can monitor the antibodies from time to time and keep from harming your small intestine unknowingly.
All that said - I am new to celiac, and am in the process of learning about it myself. I hope someone else will be along to offer you some more advice. www.celiac.org is a very informative site. Good luck!
diagnoses: mono 1972; postviral CFS 1997; fibro 1998; UCTD & osteoporosis 2007; celiac 2009
meds: Plaquenil 400 mg, occasional low dose xanax for sleep aid, artificial tears w/ ointment at night, Advil/aspirin prn and lots of vitamins