I have been battling this issue for a bit now with apple. Here's a breakdown: When restored a iPhone using a backup that is iOS 9.1 data such as imessage, app data etc is not restoring correctly. I have had this happen with both of my iPhone 6S's that were recently replaced. It appears if you do a backup using iTunes that this problem does not occur and the restore works. The only work-around I have found is IF you have a iPhone 5 backup from before 9.1 was released for whatever reason (even if it's almost 2 months old) the app data will restore using your most recent iCloud backups data.