Doug is absolutely correct. They are paranoid, but this can (and usually does) cause the "test" to be compromised. I'd say you were lucky.

Accusing someone of employing counter-measures is just one of the reasons that so many innocent people "fail". Once the polygraphist becomes an accuser, it's impossible for some people to not panic when placed under duress.

Hell, I was interrogated and polygraphed five times in three years.  Each session would last 3-4 hours and usually involved a lot of shouting. Him at me, and me right back at him. I was hooked up to the polygraph machine and asked the same question about 2,000 times. I know all about panic under duress.

Thanks for telling your story. Are you applying for a job that requires a clearance, or are you an existing employee?