I see the disconnect now... I hope (really sorry I'm doing such a poor job explaining!)
So, as mentioned, only licensed libraries will appear in the library view.
To access all the rest of the libraries you have to click on the "Files" tab in that same pane. From there you can navigate to the library and load the instruments and banks.
Another alternative is to use the trick mentioned above, where all your unlicensed libraries sit under the Kontakt Factory Library directory - I find this to be a bit cumbersome, but some folks like it.
Another alternative is to right click over on the instrument pane (right hand side)... this brings up a "Quick Load" view. You can drag all your libraries into Quick View and then arrange them any way you want. I have two top level entries, one with instruments sorted by developer, and one with libraries sorted by type. I seldom use the developer tree anymore, and may end up deleting it.
It works, and it has some advantages over the Library view - but I still wish they'd just let the full version load any and all libraries into the library view - you are not alone in your frustration!
Kontakt has a steep learning curve (especially if you want to start modifying instruments to better suit your needs), and some really frustrating "features". However, the content available makes it king of the hill - at least for now. Mach V, UVI, and Engine seem to be gunning for the crown, and hopefully competition will only make all of them better!
Does this help, I hope?