I had this issue a well when using the kobo software it would reset all my reading to "new" again.
My software indicates that I have 5 books in my library of which I think are a random 5 from the free 100. These have never been even opened on my device so I don't know where they came from. They also don't show up in my I'm Reading list when I sync.
The website and the blackberry have no idea what I'm reading and I have yet to have either of them reflect whats actually in my library or reading list.
I doing the same which is just completely avoiding the software until that's resolved.