It’s during the questions they ask to establish a baseline. You clench your toes and the concentration and discomfort that propagates all the way up the leg creates a stress response that throws the baseline off, which means the rest of the test cannot be interpreted accurately (or at least as accurately as polygraphs get).
I have to admit, I’ve never read anything about a full pain response being necessary, just a stress spike like the above. Am I out of date?