It says in The Lie Behind The Lie Detector that the 'silent answer test' is supposedly a countermeasure, but the book goes on to say that this particular anti-CM's only purpose is to catch the examinee off guard. (Other anti-CM techniques are designed to get the examinee to answer differently, thus 'catching' you.)

In my opinion, your polygrapher either suspected counter-measures or was just doing it to throw you off. If he said he was doing it to reduce 'extensive artifacts' or anything else he was (again in my opinion) probably lying.