I agree, it only works to get them apart. You may be missing something like another nut or have the wrong cone in there. Also, you may have the wrong size bearings, allowing the cone to screw in too far, which would hide the flat. I'll look at mine and take a picture of what I have later.
Looking more closely, are you sure that isn't a wrench flat between the inside lip of the locknut and the dust cap on the hub? It looks like it might be from the pictures... It also kinda lines up with the theory that you may have the wrong size bearings in there... You'll need some thin wrenches!