It looks like he has those eyes during the Mustafar slaughter and I'm guessing that one of these 3 sees him this way:
1) Nute Gunray
2) Obi-Wan
3) Padme
As for why he has eyes like that, I'm guessing that he's tapping into his emotions (anger/hate) that the Dark Side begins to consume him !!! Maul was trained from the beginning from Sidious and his emotions were visible at all times ! Sidious is the same when he's angry and Anakin is emotionally unstable to begin with, whereas Dooku is always coolheaded and is simply "technical" in his use of the Force, he is not emotional or not as emotional. I see him fighting more like a Jedi than a Sith !!!
Maybe that's the difference !!! Maybe we'll have to wait for the Lucas audio commentary on the Episode 3 dvd to get the answer for this !!! lol
Look folks, it's pretty easy to figure out. At the end of Jedi, when Vader's helmet is removed, his eyes are normal and blue (at least in the DVD release they are!). In ROTS, Anakin will have normal eyes, period. I believe that these evil eyes were just inserted for the sake of the teaser to build suspense.