IBooks transfer to PC

I have books in my iPad that were purchased a long time ago, all books bought on it are still on it. However, certain books refuse to transfer during syncing to my PC. And don't show up on my iTunes account. I have tried going into my purchased items in iTunes, but they don't appear there either

Do they show up in the iBookStore on the device? You know, iBooks / Store / Purchased.
I have different stuff on the iPad than on the iPhone so the bookshelves are stocked differently. But in the Purchased tab, ALL the books show up, local ones saying "downloades" and those on the other iGadget with a "iCloud with downward arrow" icon instead.
If they don't, I would assume that sync was somehow lost with Apple's servers and hence would explain why iTunes on the computer doesn't list them.

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