For the quests where you aquire the black books and the elderscrolls as I understand it the ids of the items you have in your inventory are not the same as in the object window, it gets some sort of quest id. If in some script you checked if you were holding the object listed in the object window it would say you don't have that item. Is there any point after you finish the quest where the item you are holding becomes a regular non quest item?
As you see I really haven't figured out the quest system at all. I'll get to it but even the tutorials make my brain ache.