What is your total completion % in the library?

[dmpdesign]

I believe you found all the royal chests.

I will look into the shrine key thing when I get home and figure out why leon is being so stubborn, and also on the library unlock event to find out why you arent seeing it in your game.

The fact the key graphic is missing from the door shouldn't affect the way it works (though I am not sure why it would be missing) as placing the key simply toggles an event counter and placing the second key toggles it another so you can begin turning the dials. ‎  I will figure out whats happening and let you know.