More the latter, I suspect. Your file is flagged "up to no good". Nobody wants to be the official that let the terrorist get away, so they all do sufficient screening that if anything happens later they can say, "There was nothing I could do to prevent that. We questioned him for a few hours, but without a warrant we needed to respect his rights and let him go."

The officials are thinking less about how this process inconveniences the traveler and a lot more about the shit storm that will ensue should they let another underwear bomber on a plane.