I had a fun SSSS experience the other day. I was forced onto Frontier because of stupid corporate travel policy for my SNA-DEN flight. I tried to check in online, it said I couldn't for "unknown reasons". I go to the counter, they print my boarding pass. I'm already used to using mobile boarding passes(you know, on other modern airlines), so I don't even look at it and head to security. The grumpy TSA agent scribbles and stamps my pass, I go through security and head to the gate. Just after boarding starts, they call my name and the gate agent looks at my boarding pass while on the phone with someone... I'm told I have to go back to security. That's when I notice the SSSS. I guess they somehow realized they missed it, but the amusing(read: sad) part is that once I get back to security and they're in the process of dumping my bag out and giving me my free body massage, one of the TSA guys is trying to figure out(unsuccessfully) who checked my boarding pass and missed the SSSS. Turns our their "scribble" system doesn't work very well. What a joke. Thankfully Frontier held the flight for me, I was the last one on the plane.
So, learn from my mistakes: pay attention to your boarding pass and point it out to TSA, because they probably aren't paying attention.