Whether it's an intentional variation, or just a much better wash in the paint job, this difference definitely exists. The first couple #50 Anakins that I picked up were fairly "clean" on his skin (head, neck, chest, arms), whereas the last few I've seen at retail are totally fried and jacked up looking. Far better with the later ones, IMO.
Not sure if you've followed the similar paint issue on the Deluxe Vader Operating Table figure, but I'd say the #50 Anakin's paint differences are even more drastic than that one.
Maybe if Jared swings by this weekend, I'll have him take some pictures of the differences so you can tell how dramatic it is. I'd definitely think it was an intentional change by Hasbro to make the figure look a lot more "battle damaged" by the fire. (the extra crispy version obviously has the later date stamps on it, btw)