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from TSA workers I know is that there's two subsections of passengers who are searched more thoroughly.
The first is "random", in that they'll search either the first or second person through their line each morning, and pull another person as they finish their first search -- effectively the TSA workers are searching someone throughout their shift.
The second are the pathetically unsubtle "red box" searches... you might have noticed at the airport, most of those little tubs for your personal belongings are gray or blue, and you may have noticed a small stack of red tubs off to one side. Very rarely, someone is told to take their things out of the other tubs and put them in the red ones.
If you are told to put your stuff in the red tubs, you have been flagged. It's a computerized screening system, not unlike the one they use to look at some checked luggage, that originates when you pick up your boarding pass. The parameters of the screen are secret (for obvious, if disturbing, reasons).
It may be little comfort, but rest assured: if you've never put your things into a red tub, you've never been flagged. You've just been unlucky.
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