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I had the same issue and called Apple support.

The representative told me to use iTunes to back. She was under the impression that selecting "iCloud" for automatic backup in iTunes would make it backup to iCloud instead of the computer.

Anyways, I followed her instructions, backed up my phone from iTunes. After the backup was finished, I told her that it backed up to the computer.

Then I checked my phone, and it was backing up too (to iCloud). Automatic iCloud backup started working after that.

So, all I did was to backup my phone using iTunes. That for whatever reason fixed backing up to iCloud.

I have had this issue since 9.0.1 (I believe)
 
I backed up to iTunes and it still gave me an error that it couldn't back up to the cloud. My iCloud storage shows that there is 2.4 gig of backup in it; but the backup on the phone shows 0, so it can't be deleted. Quite frustrating.
 
Resetting my iPhone to new seemed to have worked for now I'll keep checking to if it continues to back up to the clouds.
 
I can confirm that I got iCloud backup working again after restoring my phone.

Saying that, it is annoying having to setup Touch ID and Apple Watch again. Also, my iCloud drive and iCloud Music library didn't work straight away and I was about to smash my phone on the floor. After a couple of hours so, my music did appear on my phone again and I all my files on iCloud as well.

Though not really related to most of the people here I suppose, I am a user of the chat app LINE and after restoring my phone from iTunes, all my chat logs have been deleted and I lost all contacts that weren't pulled automatically from my contacts on iOS. LINE apparently deliberately chooses not to include their app data in a iTunes backup.

Stupidest thing ever I experienced with an app on iOS.
 
I can confirm that I got iCloud backup working again after restoring my phone.

Saying that, it is annoying having to setup Touch ID and Apple Watch again. Also, my iCloud drive and iCloud Music library didn't work straight away and I was about to smash my phone on the floor. After a couple of hours so, my music did appear on my phone again and I all my files on iCloud as well.

Though not really related to most of the people here I suppose, I am a user of the chat app LINE and after restoring my phone from iTunes, all my chat logs have been deleted and I lost all contacts that weren't pulled automatically from my contacts on iOS. LINE apparently deliberately chooses not to include their app data in a iTunes backup.

Stupidest thing ever I experienced with an app on iOS.

That is because you (I assume) are choosing not to encrypt your backup. Is that true? If so, sensitive info like passwords, health, touch id, will not be stored in the backup.
 
That is because you (I assume) are choosing not to encrypt your backup. Is that true? If so, sensitive info like passwords, health, touch id, will not be stored in the backup.

No, not true. As you rightly say, choosing the encrypted option ensures all data, even sensitive information, will be carried over. And I did choose this option to save myself the hassle of having to setup everything again but more importantly, I didn't want to lose all my health data.

Touch ID is not part of the iTunes backup - I had to set this up again. All other information (other than LINE) has been carried over. LINE works like this by default according to their FAQs. You cannot carry over chat history unless you go through some non-Apple certified steps to do so.
 
No, not true. As you rightly say, choosing the encrypted option ensures all data, even sensitive information, will be carried over. And I did choose this option to save myself the hassle of having to setup everything again but more importantly, I didn't want to lose all my health data.

Touch ID is not part of the iTunes backup - I had to set this up again. All other information (other than LINE) has been carried over. LINE works like this by default according to their FAQs. You cannot carry over chat history unless you go through some non-Apple certified steps to do so.

I wonder if iexplorer would show up your LINE info? plus any other data you may want to restore.

iexplorer demo version got me out of a pickle when I had to restore from new due to over the air icloud backups not working.

http://m.download.cnet.com/iExplorer/3000-2141_4-10968991.html

'demo has some limitations'

Hope this helps.
 
Having same issues with my Verizon 6+S.
But my AT&T 6+S for my business I have no problem backing up auto or manually.
Just my Verizon iPhone takes forever and when it's almost done in 2 hours says backup couldn't be completed. Both use different numbers and accounts. So I backed it up to my computer for now.
Very strange. And yes I've done everything except wiping it clean and starting fresh not in mood.
 
I wonder if iexplorer would show up your LINE info? plus any other data you may want to restore.

iexplorer demo version got me out of a pickle when I had to restore from new due to over the air icloud backups not working.

http://m.download.cnet.com/iExplorer/3000-2141_4-10968991.html

'demo has some limitations'

Hope this helps.

Thanks, I will give this a go - since I noticed that some app data in some of my other apps hasn't been restored as well and is lost now.

I am really concerned about this and it is a big pain in the bottom. I paid for a subscription and downloaded alot of data that I paid for and the data within the app was still available to me even after I cancelled the subscription.

This data is gone now and the app tells me to re-subscribe which I would do if the company was actually still updating their app which they don't.
 
Having same issues with my Verizon 6+S.
But my AT&T 6+S for my business I have no problem backing up auto or manually.
Just my Verizon iPhone takes forever and when it's almost done in 2 hours says backup couldn't be completed. Both use different numbers and accounts. So I backed it up to my computer for now.
Very strange. And yes I've done everything except wiping it clean and starting fresh not in mood.
My iPhone 6s was doing exactly the same thing as well as my wife's 5s and two iPads we have. This lasted at least two weeks so I was backing my iPad and iPhone up on iTunes. I had tried several different things short of wiping my iPhone clean and nothing worked. Then all of a sudden all of our devices started working again. Never had any issues until 9.0 came out. I really think it's something on Apple's end.
 
My iPhone 6s was doing exactly the same thing as well as my wife's 5s and two iPads we have. This lasted at least two weeks so I was backing my iPad and iPhone up on iTunes. I had tried several different things short of wiping my iPhone clean and nothing worked. Then all of a sudden all of our devices started working again. Never had any issues until 9.0 came out. I really think it's something on Apple's end.
It's good to know I'm not the only one. I'll wait a couple of weeks and see what happens
 
I'm setting reminders now to do an _archived_ encrypted itunes backup monthly.

I'm checking the time stamp backup daily on my iphone 6 & ipad mini 2.

I just wish somone would answer my query as to whether an app could be made to show previous over the air backups with time stamps. With alarms etc when backup not completed.
Or has apple made this impossible, it just seems such an important part of the device- the backup.
 
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