I think it has to do with the Final Five being "awakened". There's clearly no physical switch being flipped; the sudden awareness seems to be done on some ethereal level and seems to now be giving off some kind of aura. I mean, the four don't have any real proof, but "just know" they're Cylons.
The problem with that explanation is Athena's failure to recognize either Anders or Chief Tyrol when she ran into them on the flight deck. Anders and Tyrol were already self-aware at that point.
I think most of the Cylons are incapable of detecting the Final Five, except for Caprica Six and the Cylon Raider(s). There has always been something different about Caprica Six. She's the only Cylon who sees an imaginary figure that she believes is real. (Maybe she's right.) She has had self-doubt about her identity even though she knows that she is a Cylon and always did. (At first Boomer didn't know she was a Cylon. Then she began to have doubts about her identity. Now she seems to have turned her back on humanity completely, though this could change.)
As for the identity of the individual that D'Anna apologized to, it's very possible that it was Saul Tigh. It makes perfect sense. But I'm still open to the possibility that it's someone else.