This could totally just be my own weird problem, but I find that sometimes marks left with carbon paper act as a "resist" when I go to put paint down. It seems like carbon should be carbon...but I wonder...I still use the "scribble method".
I use Sally's graphite paper by Saral. It says "wax free" on the package. I never have the "resist" problem with it. I wonder if it's the brand you are using...?