Pillpopper,

What you are describing makes perfect sense.  I have read through some polygraph literature (can't direct to exactly which publications, don't remember) that describe the machine as recording reactions to questions not based on truth vs deception but rather the level of THREAT the question poses to you.

Assuming you don't know the difference between relevant and control questions and you are not lying on the relevant questions, the examiner expects you to be more threatened by the controls.

Once you know the difference, however, the relevant questions will always be more of a threat to you simply because you know these are the questions you should not respond to.  This is really true by default - whether you are lying or not doesn't seem to matter too much at this point.  Worrying about not responding only causes you to respond... and fail.

This is my theory - this is also why the polygraph is lame.  Sorry to hear about everyone's trouble - I've experienced the same things for the same reasons.  Good luck.