Kind of blows having auto backup to iCloud then having issues that the solution is "don't use your backup"
I've been finding after talking to some other folks that moving from an older iPhone on iOS 5 to a new iPhone 5 on iOS 6 has caused corrupt backups. I updated to iOS 6 on my iPhone 4 and backed it up before moving to iOS 6 on my iPhone 5 and I haven't had any issues.