I'm just going to throw this in here, hoping I'm understanding your problem and it helps. If not, disregard.
Download drobpox to your computer, then the app (free) to your ipad.
Now, any book you want on the ipad, move to dropbox (it must be in epub format, but you cand do that with Calibre) .
Open the dropbox app on your ipad, and click on the book......it will download and say "cannot read this file", but just click the arrow on top, and that will give you a "open this in IBooks?" option. Click "yes" and there is your book.
This is how I download all my books to my ipad, and I've never bought one from Apple.
I've also gotten the latest update to ITunes, and am having no problems this way.