This is an email I just sent to the TSA:
I flew to Newark yesterday and got stuck there for 4 hours waiting for my flight back home. I smoke and Newark has zero lounges to smoke in after you go through the check point. That forced me to go through the checkpoint at least twice.
My boarding pass also got flagged for your special screening plus pat down. It was a little surprising at first, but completely unexpected the second time I went through seeing how they already did it.
There's two problems here: the lack of smoking areas behind checkpoints and when passengers are selected to get the special treatment. The first is fairly easy to fix, and it should be addressed since I had the same issue at Indianapolis before I went on my first flight.
The second one is a true security issue. I now know how my boarding pass gets marked for the special treatment, SSSS. Suppose that a friend and I were plotting to bring some explosives on board. One of us gets the SSSS on our boarding pass and so we swap bags.
The one with the SSSS would get the special treatment every single time he went through, but the other one w/o the SSSS would just walk through the metal detector and xray machine. His bags would never ever have the possibility of getting swabbed down for explosives.
The problem is that the random selection happened at check in, and not at the security check point. This issue could be corrected if the TSA agents had some random counter or something that told them to pull this bag and person over. This would result in a greater percentage of passengers getting the special treatment.
The above would have eliminated the duplicated effort expended on me while at the same time making the swab down and frisk more effective by not wasting it on smokers who are forced to go in and out.