Incomplete iTunes backup?

Hi everyone,

I'm having hard time backing up an iPhone 6 Plus 128GB (iOS8.1.3) connected to iTunes 12.1.1 64-bit on a Windows 7 Pro x64 machine.

After performing a local encrypted backup via iTunes, the backup folder on PC takes roughly only 3.6GB of data, when there are 65GB used from iPhone storage. Also there are no media files transferred during the backup process, no Photos, no Videos, no music files; and there's also the Secret Folder & Photo Video Vault Pro app in which are stored 43GB of media files that are obviously missing.I assume that's safe to say no user data is transferred at all in the backup process.

I already trusted the access between iPhone and PC, I authorized iTunes to transfer the purchases, the apps are downloaded just fine in iTunes - but the thing is that if I restore this "incomplete" backup on a new iPad Air 2 128 GB (iOS 8.1.3), all the apps together with Photos, Videos and Music library are empty of data.

Any help would be highly appreciated, thanks folks!

P.S. I had no data missing or other issues when performed a similar backup process from an iPhone 6 64GB on the same PC.