They changed how it works for Kontakt version 5.6.8
 
I really don't recommend using any Kontakt Library Maker tool.  NI has to generate a license key for a license to correctly show up in the libraries tab.  These methods (and I guess now a "tool") of hacking a normal Kontakt project into the Library tab can cause all kinds of problems with NI's Service Center and (I'm guessing) Native Access.  Best to leave that to the pirates, if you have a legal licensed Kontakt this will only cause you trouble.
 

I installed the new OTS Hollowbody library BEFORE updating after seeing this thread.
 
After I updated I revisited the Looploft Drumdirector library that steadfastly refused to regester using the old method. Using this new method with Native Access it regestered without issues. As I would have had to log on to service centre or access to regester a library in anycase I don't see a issue FOR ME with the new system, if anything it makes the process a little slicker.
 
Type in the serial number, regestration done, navigate to the folder in Access and the library is added.

msorrels
They changed how it works for Kontakt version 5.6.8
 
I really don't recommend using any Kontakt Library Maker tool.  NI has to generate a license key for a license to correctly show up in the libraries tab.  These methods (and I guess now a "tool") of hacking a normal Kontakt project into the Library tab can cause all kinds of problems with NI's Service Center and (I'm guessing) Native Access.  Best to leave that to the pirates, if you have a legal licensed Kontakt this will only cause you trouble.
 

Why not just use Quick Load? I tend to do that for my most commonly used libraries even if they are regestered, its easier than the libraries tab once you have set it up. 

Quickload is the right answer but users do seem to like having things show up in the Library list.  NI has been steadfast at reserving that for products that pay license fees.  I think the way this new Kontakt works will be just fine, it's just different.
 
The biggest problem with Quickload is it doesn't update if you move/change things.  And Kontakt has no maintenance features.  On Windows (not sure on Mac) it's just a bunch of directories with file links to the .nki/.nkm files stored in %LOCALAPPDATA%\Native Instruments\Kontakt 5\QuickLoad
 
I've often considered building some tools to manage the Quickload links, so you could have a list of directories that you wanted maintained in the Quickload and it would remove the existing dir and rebuild it fresh.  Which I have to do now when I add things/move things.  My Kontakt content is split up into directories by publisher/producer, then by Product.  So I get a new (non-library) product, I add it to the Publisher's directory but then I have to manually update the Quickload for that publisher by deleting and re-adding their directory.  Tools could be built to do that for me.  As well as find (and remove) bad links/etc.  But other side projects have been more interesting lately but it's on the list.  I may get to it if NI doesn't do something themselves first.