I've always had sinus/allergy issues...it was an ongoing problem for me, even before the RA. I was on mtx about 8 months I think, and seemed I was just living on antibiotics. We stopped the mtx to do a 3 week antibiotic treatment for chronic sinusitis, with the intention of going back on when it was finished. the rhuemy ordered a Cat scan of my sinuses as well as giving me some different allergy meds. That was in January, and last month doc actually said that since I had been off the mtx, she hadn't to put me on any more antibiotics, so we should just leave well enough alone for now.
Personally, I think if you have been having this much trouble for this long, it's worth a call to the doc. Maybe it has nothing to do with the meds, but you sure do ned to feel better!
Take care, and let me know how you're doing!