Well in this case it did actually indicate something other than the passage of time, it indicates the player was using a shoe operated cheating device an remarked on how he would normally move more quickly.

Maybe I overemphasized the first move because it was emphasized in the article, in general cheaters use their clock in weird ways throughout the game since for them pretty much any move is similarly complex. In this case the shoe operating cheating device raised the minimum time to make a move, which is a characteristic common to many forms of cheating.