How much prednisone are you taking? Even when my gut was in remission, my arthritis was flaring. I have been on prednisone for a year and a half straight and we have yet to get the arthritis under control. It has actually gotten worse lately even while on prednisone. The methotrexate should help with the arthritis, though, so I would talk to your doctor if you're still having that much trouble. Maybe you aren't on a high enough dose of the pred or mtx.
Crohn's Disease, Acid Reflux/Gastritis, Hashimoto's Thyroiditis, Endometriosis, Arthritis, Depression/Anxiety. Too many meds to list them all. =)