I updated to iBooks 3.0 on my iPhone 4S and iPad 2, both running iOS 6.0. Everything is fine on my iPhone, but on my iPad the "Purchased Books" collection is empty. The books I had downloaded were in my Books collection and the all books show up in the purchased area of the store, but nothing shows up in the library purchased area. In addition, some books I had downloaded showed as not being installed in the purchased area of the store.
I tried deleting all books off my iPad, but that didn't help. I noticed the books I deleted off my iPad showed up in the books area on my iPhone (but not downloaded). When I delete books of my iPhone it asks me if I want to delete them off all devices, but I don't get that option when deleting books on my iPad. Despite that, collections do appear to sync, though not instantly, and deletions on the iPad do eventually show up on the iPhone.
I tried removing iBooks on my iPad, restarting the iPad and reinstalling, but that didn't fix the problem. It also didn't remove any of the PDFs I had on my iPad. It also seemed to cause the books I deleted on my iPad to show up on my iPhone.
It seems like my iPad's book area is corrupt somehow. How can I fix this?
The iCloud restore finished and I update to iBooks 3.0 and now everything works, so it looks like a restore will fix this. I did initially set up as a new iPad first and test iBooks. I don't know if that was required or not, but since it doesn't take much more time it might be a good idea to try.
Here's what I did:
1. Set iPad into DFU mode (because it wouldn't boot, dunno if this is needed)
2. Restore iOS 6
3. Set up as new and install iBooks and test (works)
4. Go to Reset -> all media and settings
5. After reboot restore from latest iCloud Backup and wait a long time.
6. Upgrade to iBook 3.0 (works)
I haven't synced with iTunes yet so hopefully that doesn't break it. I'm still convinced it broke do to a bug when upgrading from iOS 5.1.1 to iOS 6 OTA, but this will fix it.