I would like to answer about one of the causes that could lead to this complex situation.
I had a GPT system with Ubuntu 14.04, no Windows. I was unable to install Windows without wiping my disk. So, I took the necessary BACKUP (always do that no matter what simple thing you are doing) and wiped the disk using bootable Windows USB.
Now, the catch is, even if this automatically converts from GPT to MBR, somehow, it keeps signatures of GPT. So, any tool for managing the hard disk (like Gparted) gets confused as it founds GPT and MBR both. So, this will show all the disk space as unallocated as if you do NOT have Windows. But, if you check in your media, it will show the mountable drives, even, it will show all the data that your drive has.
Solution to this is - make a bootable USB with any Linux version. Live boot it and once the Linux starts, open the terminal and use gdisk utility to remove all corrupted GPT entries or Signatures.