I now have two copies of this book ..The marker in the dungeon still remains on the chest even after I take it.. Where does it go ?? Mabye it might clear that way..

Ignore the marker and take the book to the Orc librarian at the Mage's College. See if it gives you the option to give him the book. IF it does not may have to back track to a previous save or let the quest rot in your journal.