OK, I see you found a solution while I was double checking mine.
When I connect my Kobo to a Linux computer I don't see a kobo folder, but when I connect it to my Windows XP laptop, I see a .kobo folder along with a couple of other dot-name folders and the Installers folder.
The .kobo folder is a private folder which has the database in it, and a few other files needed by the reader software. I put my epub files outside all the folders and they get found and processed. If you have put your books inside the .kobo folder try dragging them outside so that they show up along side all the folders. Then do a software eject before you unplug the Kobo from the computer. It may take quite some time to do all the processing, but eventually all your books should show up. Please let us know how that works, or if we haven't understood your problem.
Last edited by pholy; 06-30-2010 at 06:36 PM.
Reason: He 'fixed' it himself...