There are one or two 'hidden' files on the card and it appears you never copied them over.
Go here
http://www.recuva.com/ and download and install the programme, it's free. It should recover any lost files or folders from formatted discs/cards, providing the data hasn't been overwritten. You may be lucky.
You need to go to My Computer - Tools - Folder Options - View - and select Show Hidden Files and Folders.
If you can recover them just copy and paste into the folder you placed the card data backup, and also copy onto your SD Card.