Sorry, but... this is by design. The purpose of global layers is to be the same as if you copy-pasted all the instances on the layer to every other layer it represents. (This is what you were forced to do for things like HUD layers before this feature was added.) The process ignores the properties of the object. If you have global instances on that layer they will be re-created because that's what would have happened if you copy-pasted them to the other layers too. I'm not sure why you would make the objects on a global layer also global though - you don't need the layer to be global if you want the objects to continue existing between layouts. So it seems like you want one or the other, but not both.
Also we can't just shrug and change things like this, because it could break existing projects which rely on the existing behavior.