While there are no scientific studies on the influence of irregular heart rates on polygraph outcomes, because of the way polygraph "tests" are scored, one wouldn't necessarily expect such a condition to significantly influence the results. However, it is important to bear in mind that polygraphy has not been shown through peer-reviewed research to reliably detect deception in people without any heart rate irregularities under field conditions.

The consensus view among scientists is that polygraphy has no scientific basis. A statistical analysis (255 kb PDF) conducted by Dr. Alan P. Zelicoff on data from the best published field studies suggests that "if a subject fails a polygraph, the probability that she is, in fact, being deceptive is little more than chance alone; that is, one could flip a coin and get virtually the same result for a positive test based on the published data."

I wish you all the best in the hiring process, and hope that the polygraph won't end up wrongly disqualifying you.