I'm with Ceric. Sylar was able to tell that the first guy he killed had powers of some sort. He didn't know what kind until he investigated, but he knew the guy had powers. After that, he killed people on the list because he could find people using the list much easier than searching them out, not knowing his targets until he could see they had abilities.
Now then, on the surface, what opposes what I'm suggesting is what happened with Claire, when Sylar tried to kill her in Texas. However, with both Claire and Peter in the room at the same time he was there, there is a chance that he was confused for a short amount of time, and then realized his mistake right away when he looked at the extra cheerleader.
It's hard to say if he has trouble detecting who is the individual with powers when the person is not on the list, as he went after Claire because of the news of her saving a man in a fire. Perhaps he could tell people with abilities were around, but is not able to tell which person he can tell is special. I don't know, but it makes sense.