IOS 9.3 sorting not working

I went back to 9.2.1 and resynced all the books. Took around 12 hours due to the "waiting for changes to be applied" bug at around 10 mins per time and the failure to copy more than around 100 books at a time before sync gets cancelled - also a known bug - which meant around 50 syncs to copy them. I then discovered that around 300 books simply would not copy - they'd appear on the iPad and then disappear once the sync completed. Ended up deleting the entire collection of books from the Mac, reloading them from scratch and re-syncing the lot again, another 10 hours or so. All works now and I won't be updating the iPad beyond 9.2.1. Apple has a disgraceful reputation for leaving people in the lurch over things like this. (And simply dumping technologies - Newtons and HyperCard for 2 examples, there are many more.) Both the above syncing problems have been well documented for years and have just been ignored, just as the dumbing down of iBooks has been. Simple to fix but Apple can't be bothered.

Close iTunes, turn the iPad off and restart it and do a fresh sync and see if that fixes it. Remember that only a hundred or so books get copied over at a time despite the sync showing hundreds of them being copied before the sync cancels - assuming that iPad bug is still there in the iPad2 - so you'll have to keep resyncing it until all the books have actually copied over. Probably worth doing what I did - make a backup copy of your iTunes or iBooks books folder, delete the lot from iTunes/iBooks on the Mac or PC, reload them from your backup copy, then do a "restore from backup" for the iPad and go through the numerous resyncs procedure until they are all copied over. (Note that you'll have to resync them all to any other iPad or iPhone that is linked to the same books.) All my categories etc were preserved despite the deletions and the books appeared in their proper places on the iPad once restored. I also did the 'backup now' in iTunes, then 'Erase all content and settings' from the iPad's Settings/General/Reset prior to the 'restore from backup'.