Sometimes iBooks is very slow to download books and you may have to wait longer than you think you need to.
Also, the books go to a certain catagory within iBooks ... have you searched all your "shelves"?
Sometimes, you need to turn everything off and reboot the iPad to make it behave...
If none of the above helps, I've got no idea what's happening, because I, too, get iBooks to open a nook through Goodreader.
Sorry.
Marilyn
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