Physiological changes ("responses") measured by the polygraph instrument that occur during a time frame beginning with the asking of a question and ending with the beginning of the asking of the following question are considered to be associated with the first question. Thus, to answer your question, no, it doesn't matter whether reactions occur during the polygrapher's asking of a question as opposed to during/after the subject's answering.

Whether or not a response to a relevant question is deemed to be indicative of deception depends on its magnitude in comparison with any physiological response(s) to an associated "control" question. See Chapter 3 of The Lie Behind the Lie Detector for further reading on how polygraph charts are scored.

I recently took a pre-employment polygraph and was told that I had one issue with one of the questions:

My polygrapher said that I was "responding" to one of the questions, but kept asking me if there was something about the way it was phrased that would  make me respond.   

My question is -- is there a difference between the timing of a reaction and what it is supposed to indicate?  I got the impression from his statements and what he later told me that he didn't think I was lying about the answer, just that the way it was asked I "responded."  Is there a difference in terms of what that would look like on the charts, or did this guy just think I was honest Joe? Would there be a difference between getting weird reactions right after the question is read vs. during/after an answer?

I hope that question is clear enough...