Just an opinion -- if a doctor told me I had Lyme's Disease, I'd take the antibiotics no matter what the general practitioner thought.
Hey jcard, you must be the same person as jmc...... Did you find a solution to this problem? Was it Lyme's? I am asking because I have similar issues and no solution.
Lyme is very hard to diagnose. Some people go years before getting a correct diagnosis. In this case, where you have a conflict, I would ask, were either of the docs specialists in diagnosing and treating Lyme? Your primary care doc isn't a specialist in anything, he's by definition a generalist, and you don't mention the other doc, but when you get a conflict it's not a bad idea to see a third doc and one who really specializes in what you think you might have.