pillpopper,

I absolutely agree with you.  In fact, from an examiner's own mouth - the polygraph allegedly works by determining which questions are most "threatening" to a person.

If one understood the idea behind control questions (choosing to not attempt countermeasures), which questions would be more threatening?  At this point it isn't between deception and truth!  For this candidate, it is simply knowing that a control question won't get him/her disqualified but a relevant question could!  During my exam, that's what I found myself thinking about - not "hmmm, did I exceed the agency's drug policy?" (I didn't), but rather "shit, this is a relevant question - I can't react or I'll fail" (reaction given).  

Seems pretty unfair to me.  Examiners - is this not at all the way things work?  Please enlighten us because I genuinely would like to know.