Copying and pasting the bookshelves tends to be problematic; the resuling objects, as you have noticed, tend to not function properly. Instead, I'd recommend creating one from scratch.
Creating an interactive bookshelf from scratch involves:
Placing the actual bookshelf object.
DefaultBook objects on the shelf.
PlayerBookshelfClickTrigger trigger with the bookshelf object (the in-game one) selected. Resize the trigger volume to cover the surface of the shelf you are making intractable (this trigger is the thing a player will actually interact with in-game).
PlayerBookshelfTrigger trigger (with the bookshelf selected again). Resize this trigger to fill the volume of the shelf and enclose the books, more or less.
Using the Link References tab available by double-clicking the bookshelf container, add reference links to each book you placed above. Use
BookshelfN (where N is 1 to 18) as the keyword for each link.
Similarly, link the click trigger to the container object. The keyword is
BookshelfContainer. In the primitive tab, make sure the trigger supports player activation.
Link the other trigger to the container; you don't need a keyword for this reference. Ensure, in the primitive tab, the trigger type is
Finally, link the container back to the trigger above (not the click one, the regular one). Use
BookshelfTrigger01 as the keyword.
That should cover the basics. For extra credit, you probably want to set up collision barriers between the placed books so they don't move around, and hide the actual container object outside the world slightly. You have to repeat this for each shelf. It's a bit tedious.
If you really want to try to debug the cloned bookshelves you've created, I'd go through the above steps with them and make sure all the links are in place, and that your click trigger volume is accessible, and so on.