Used to own an 1860 era victorian house. Went on trip and came back to find my spouse has allowed entire washing machine load of water to spill out onto floor. What this has to do with your question is that the washing machine was on the first floor of the house. The room had square flooring tiles upon which cheap roll carpeting has been placed, this over the original wood. To glue the square tiles down, a black gunk glue was used. Perhaps your black marks are really tile glue which did not get sanded off when your floors were redone. With the washing machine water soaked into the rug and tile, this all had to be removed. Yes it was a mess BUT, found out that the black gunk was water solible. After removing the wet rug and prying up the raised tiles, I placed newspapers on the floor to help soak up the water. Along with the wet newspapers was some of the black gunk. I purchased a trowel the width of the flooring plank and was able to scrape up the now softened black gunk. Was able to make the floor look quite nice with the scraping method. The floor through the years was very "rolling" and sanding, the immediate resolution of most people would never have worked. I'm not recomending that you dump a washing machine load of water on you floor, but a more controlled situation may be what you need to do. Good luck.