Check the All Books collection closely.
Normally a new book gets added to the Books collection, but I've had one or two that only showed up in All Books after downloading, until I manually moved them.
Since I normally keep all new books, and books I'm planning to read in the Books collection, it took me a while to figure out what happened.
If that's not it, then please give a detailed description of what you've done, both on the iPad and the computer in iTunes (if that's what you meant), and the type of computer (PC or Mac). I kind of think I know what you're talking about, but I want to be sure before I start guessing at possible causes.