The last poly I took, after the first run through, the examiner told me "you are controlling your breathing" and I laughed and said I am just trying to stay calm, like you said.  He just shrugged  his shoulders and we continued on.

It sure sounds like you're screwed. It is not common for a polygraph operator to accuse an examinee of using countermeasures (let alone to name a specific type of countermeasure) in the absence of a genuine suspicion. Your breathing may have been too slow, too deep, too regular, etc. in the polygrapher's opinion.

If your chart was otherwise passing but the examiner thought you were using countermeasures, he can indeed effectively fail you. Your chart may be deemed "no opinion" with a note that countermeasures are suspected. In effect, this will be treated as a failure--or worse.

Ok, I took my polygragh today in Ohio and the examiner accused my of breathing countermeasures after the first chart. After the the last chart, he said I was not helping myself, that I was being deceptive, then asked me to leave. 

Is this kind of confrontation a bluff or am I screwed? What if my chart looked good but the examiner thought I was using countermeasures? Can he still fail me?