EDIT: PLEASE SCROLL TO LAST COMMENT for update on issue. I've found a way to highlight this much more simply.

I have only tested this in Minecraft 1.9 and do not know if it is a persistent issue in other versions. Below are the steps to replicate the issue.

1) Set up a redstone system so that an item will go through a hopper, into a dropper, into another dropper, and then gets spat out and picked up by the player
2) Make several copies of the same book, for example, "Title- Copy of Original by Player"
3) Line the hopper with clones of this book, and fill the first dropper in the series with clones of this book, leaving room for a few more books to flow in
4) Allow the redstone circuit to proceed, pick up book at the end of redstone system

The book no longer stacks with identical books. This issue subsides once you actually try to read the book- they all start stacking again afterward.

I am not 100% certain where in this system the issue occurs, but I am guessing it could happen in any transfer of the books from one non-player block to another.