Copies of written books cease to stack after a while

I have made a build that requires KeyCards to access it. Its made using written book that is copied into several copies, some of which are used to make the sorting system that will accept only the same book (that I previously checked to make sure it stacks). It works for a while but then suddenly the books refuse to stack anymore and I have to remake them and switch out the new ones with the old ones. 

It is worth noting that I store the Original and my Copy of Original in my EnderChest and take it out when I need it.