Did you see marhis's comment below? She's created a fix for that issue (and provided a link to it).

It makes sense for the Shifting Paradymes, doesn't it? Did you give them the tats they wear when the game begins? I know that was the original purpose of the overlay (so those tats would "stick").

Is it that obvious? Yeah, I'm sure it is. :P (But there's a little twist, also. You'll see...)