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I've found iCloud backup to be pretty much bulletproof - fast, reliable, painless, and it happens every time you put your device on charge. I was never happy with wifi syncing via iTunes so I stopped using it; perhaps you should too?? Life's too short to get all vexed about this stuff. If it doesn't do what you want, dump it and move on - there are alternative apps for just about everything; I was only syncing regularly for podcasts, and I use Downcast app for that now. I never used iBooks because Kiindle had/has a much better selection where I live, etc..etc..