Hi Joanne,
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!
Jody