Believe it or not I just saw a board that had this exact problem. It was a white based Gnu Street Kills and the kid had waxed it with a red wax, scraped it and the wax had absorbed so much into the board he couldn't scrape it off. Brought the board to me to see if I could fix it. Almost looks like a color bleed from the base graphic but after some serious scraping I got some more red out but it's still there.
(Ignore the excess wax you see, this is before I gave it a thorough scraping.