Can't see all books

Is there a catch to getting Calibre to recognize all my books ?

Lets say out of 400 books, (90% are EPUB) but when I add to Calibre, I can only see 100 of them.

My current file layout is as such:

D:Books/Fiction/(Author or Title Folder)
D:Books/NonFiction/(Author or Title Folder)
D:Books/Comics/(Author or Title Folder)
etc

eg: D:Books\Fiction\Andy Weir\The Martian.epub
D:\Books\Fiction\DragonlanceBooks\ (lots of books)

Library folder is
D:Library

Is my layout causing the problem or something else.... ?

Any info/ideas appreciated :)

Cheers
:help: