Just had the same thing happen on my way home from Australia. Got pre-check on the US outbound, used SmartGate to get in to Australia.
No problems with Australian exit controls or security, but when I got to the gate, I was pulled aside (with about 5% of the other people on the flight, by my estimate) and I got an explosives swab and a very cursory patdown. Sure enough, I had an SSSS on the bottom corner of my BP that I hadn't noticed before I was pulled aside. I assume it was a random occurrence.
I was on an Australian carrier.
ETA: Looks like this thread also discusses the issue:
http://www.flyertalk.com/forum/check...ry-member.html