Happened to me.
This process creates a clean files system. It appears that iBooks file area is cluttered with unfinished business. With iBooks excluded from the backup, the problem goes away.
1) Backup your iPad to iCloud
-- Turn on iCloud Backup if it is not already on.
-- Under "Backup Options" deselect iBooks (make sure everything else is selected)
-- Delete the iBook App
-- Tap "Backup Now" and wait for the back up to complete.
2) Reset your iPad
-- make note of your AppleID and Password in iCloud
-- turn off "Find My iPad"
-- goto Settings-->General-->Reset
-- choose "Erase All Content and Settings"
3) When the iPad starts, choose "Restore From iCloud Backup"
4) Reinstall iBooks
5) Download your iBooks from "Purchased Books" collection.
Hope this helps.