Have you tried opening a support ticket with Kobo? This actually sounds more like a corrupted database OR a bad book that is preventing others being added.
eMail:
help@kobobooks.com
http://www.kobobooks.com/help
http://getsatisfaction.com/kobo
http://kobo.zendesk.com/home
are all viable means to get in touch with Kobo and ask for support.