If you look back at that scene, it showed a closeup of Anders' eye and there was a subtle flash behind the eye. I gathered it was Anders sending a signal to the raider to back off.

I disagree for two reasons:

1) The raider clearly scanned Anders. The "eyebeam" on the front of the raider locked in and scanned Anders' face. The flash I think was merely an effect added to convey the sense that the scan detected that Anders was a cylon.

2) Anders was decidedly confused about WHY the cylons broke off the attack. If he's been "activated" then I think it's pretty weak to suggest that they're all aware that they're cylons, but that they haven't had their "purpose" programming activated - that's like leaving a computer running all the time, burning electricity and risking hardware failure, while never actually using that computer to do any kind of work. What is the logical reason that the final four would become self-aware, but be awaiting their "programming" that determines what they are supposed to do? So if Anders sent the cylon a conscious signal to break off their attack, why would he later be so agitated and confused about it?