Miller, you are correct when you state that you should create a reaction to all "control" questions when employing countermeasures.

Polygraphers assume that everyone has "stolen" something from an employer--this includes paper clips, pens, etc.  

I wouldn't go too far in attempting to explain a reaction to this question... Something along the lines of "I remember the look on my mother's face when I stole some nails from the hardware store when I was 5..." or "I was just using a pen today that I brought home from work.." would work well (assuming that these were trivial admissions that you made during the pre-"test" interview)...  Just be sure not to make any type of damaging admission (major thefts, embezzlement, changing your story, etc).

Also, keep in mind that questions pertaining to theft can also be relevant as well.  If you are asked "Have you ever stolen an item worth over $200?," the question is now relevant.  Here, you obviously would not create a reaction (nor would you attempt to explain a reaction should the polygrapher accuse you of displaying one).