All you have to do is use the console command to drop the book, and pick it back up. It will then register that you found it.
Annoying yes..but it works, I just did it for the "Legendary Scourge" book.
I went back to where the book was located when I found it (quest marker showed it)..and dropped it...but I don't think it's necessary to do that.
Try this in the console:
player.drop 0001AD18 1
Then pick it back up.
Keep in mind that code there is only for the OP's book. If you are having the same bug with a different book, look your book up here: http://elderscrolls.wikia.com/wiki/Console_Item_Codes_%28Skyrim%29