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.