I got a notice to update. Great, I updated to version 1.2 .
At first I thought all my books and magazines disappeared. After a while they started to show up, but all of my magazines which are PDF had the same cover as the first one. Underneath that cover was the original magazine.
I used the new feature of creating a new lib (this is great), and moved one of the magazine to the new bookshelf. Guess what, all the magazines moved with it, with the same cover.
I did not used iTune to update or sync. Just downloaded directly, and prompt it not to sync.
I also noticed that there is a new way to delete books, and away to move books to other shelves. For the life of me, I couldn't find a way to delete a new shlef I created. Maybe it needs to be clean first.