Most likely because the tool you are using isn't very good for stuff like this. I know, it's weird, it creates the partitions and all of that, but something about the Windows tool that just messes things up. I've had the exact same problem on another phone. Typically gparted is recommended for these kinds of things. You should be able to set up a Ubuntu Live CD or bootable USB drive to use the gparted tool there.
Though if you have a newer bootable Ubuntu version, you won't need to install gparted.
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