Hi, I know this is a late post to this thread, but I'm gonna do it anyway...the addition of color by annatto is influenced by a lot of things. Yes, it does get darker when you separate the curd from the whey, and yes it does deepen with age of the cheese since (all other things being equal) as the cheese ages, it dries slightly, which means it contracts and therefore you have the same amount of color in a smaller package. This last is because usually the cheese gets more acidic as all the remaining lactose is eaten by the bacteria, and annatto responds by getting darker (kind of like the phenopthalien dye in acid test-kits changes color depending on how basic/acidic the solution is)
Hope that all made sense!