Have you considered that you might be allergic to something in either the Armour or the Allegra? Fillers in drugs often cause people side effects. Also, if you've been hypo recently, and the long, cold, dry winter has just ended, could it be a secondary skin problem that hasn't been able to heal?
I've never heard of antibodies causing any symptoms (doesn't mean they can't), except, of course, destruction of the thyroid.