What do you mean, "a couple of my libraries"? You just said you only copied ONE library.
No books come with calibre (except for
one copy of the Quick Start guide.)
What structure are you not seeing, and why did you expect to see it?
Do note that preferences are NOT stored in the library, if you want to copy over the preferences you will need to take a look at this FAQ entry:
http://manual.calibre-ebook.com/faq....backup-calibre
And copy over the %AppData%\calibre folder to the new computer.
I do not understand what you are seeing, because you are being confusing in the way you describe it -- and that makes it hard for me to help you.