How to recover PDF files from iCloud to iBooks?

After iOs 5.1 upgrade I can't recover my iBooks PDF files. I made a wifi backup to iCloud before the upgrade but I can't recover them. In backup options iBooks says(584MB).I think the 584 MB is proportional to the ammount of PDF files that i had prior iOS 5.1. Please help!!!. People I need your help those files are important. Everything is turned ON in iCloud Settings.
Again when i go to iCloud>Storage & Backup > Manage Storage > My Name iPad --------> It says bellow Next Backup Size iBooks 584 MB

Thanks - I've gone into settings on my iPad for both iCloud and iBooks and can't see any settings that say that these PDF documents are/can be backed up there?
If I go into iBooks on my mac book (yes-running Mavericks) then I can see all the collection titles I've created to file these PDF's but none of the files underneath them?
The purchased ones from the iBooks store naturally show up but my other PDF's don't

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