This is an excellent question.
My personal belief is that Justine was not infected from the beginning. Instead, I think she became infected sometime between Ghost Story and Cold Days.
First, we know that Justine truly loved Thomas and he truly loved her back. This, and in particular the moment of self-sacrifice made by Justine, granted her protection against the Raiths. I do not think that a Nem-fected person could acquire that protection. For example, Harry was never granted that same protection from his relationship with Lucio. Even though Harry loved her -- Harry falls in love very easily -- Lucio never truly loved him in return. Lucio couldn't because her mind was not fully her own.
Justine looses that protection sometime after Ghost Story. We THINK that we know how and why -- Justine and Thomas essentially cheat on each other on purpose to break that bond, and then re-establish it. But, is that actually what is happening? What if Justine LET Nemesis in, not understanding its nature, but believing that it could give her Thomas back (which of course, it did). Perhaps this is the reason that Uriel didn't mention Nemesis or notice the presence of Nemesis in that scene.
In Cold Days, I believe that Justine was Nem-fected. Maeve believed that she would kill Lilly, take Sarissa away from Mab by placing her with Summer and if Mab took retribution by killing Maeve in return would only pass the mantle to the pre-nemfected Justine, who was also on the island. Maeve messed up by not realizing that Mab's back-up plan was also there -- Molly.
