I've noticed this a lot while flying as a pax in the last year. When I've recieved the dreaded SSSS on my initial flight, the next leg never has the SSSS mark. I'm guessing it means that the airlines assume you will just be going to your next flight, and not going outside to smoke or get something out of the car (that your partner drove up and left while you were in the air, or something).
Might be something for the airlines to consider...
RD