I think the problem is how many files are in the images folder.
Whenever it's close to 7500 it can't create more pictures (you can't even add more files manually when the Kobo is attached to your computer, Windows 7 gives "an unexpected error"), and all new ones will become ghosts.
My advice is to delete all unnecessarry pictures:
This way you make space for more new books.
I'm still not if I should keep my Kobo, some things are pretty good on it, but some other things are done WAY better by other readers...