Having just spent the weekend wandering around the US on a strange itinerary, I got the dreaded SSSS on the first boarding card of each batch (I had 6 in total, issued in pairs and the first of each pair was SSSS). On each occasion the TSA staff were very polite, thorough and competent.
On one occasion I was in transit airside and rerouting at an Admirals Club when an SSSS boarding pass came up for the next flight. The Admirals Club receptionist said that I would have to exit security and reenter to go through the secondary screening, otherwise it would be flagged at the gate and delay everyone's boarding.
This was irritating since I was already secondary screened at the preceding airport , but the receptionist very kindly made it easy for me by recommending that I left my bags and coat in the Admirals Club while I went back out through security, thus making the whole process much quicker.
I can't help feeling there was a logic failure here somewhere.
