Werewolves are not dead. They are just infected with the Werewolf virus that turns them. Vampires are dead tho. I think it is because they are both supernatural beings that they can see her
I think it has a lot to do with Annie's self confidence. When she is feeling really confident she can be seen, which takes a while to build up. But then when she has a knock-back she cannot be seen again, apart from by George and Mitchell, whom she is comfortable with