Its only happened to me on SSSS situations, never for cert upgrades. In fact, for certs I've just been called at the gate to hand them in when I got there, like an afterthought.

I only get SSSS'd rarely, though, and it is really funny when it happens as I have an airport ID badge, which is what I use when flying as my ID (only from that particular airport). They're always giving a double take.