Rearranging iBooks on bookshelf manually
Are you doing it through the categories of purchased books or PDFs or collection? Try doing it through the collection. 

Another thing you could try is go to your iPad's Settings, click on the Settings icon and scroll past the General settings and other apps until you see iBooks then click on where it says "Show All Purchases" and slide it to No. Then try rearranging again from your bookshelf collections. 

I have no idea why it worked for me. I had your same problem with rearranging with the edit on and then when I clicked done it would revert back to the original unwanted order. But the steps I just described fixed it for me. I will now try and reselect show all purchases and see if it undoes what I just "fixed". I do not even know what made me take those steps - maybe intuition. But it worked like a charm.