Select your upper layout and make sure it's "Transparency" property is set to yes. By default the first layer created is not transparent. If you create a layer over it the new layer will be transparent by default, but adding a TiledBackground object on it will cover the under layout. If you just switch the layer's position, it means that now, your upper layout is the one being not transparent with a sprite, covering the transparent layer with the tiled background object.
This is unlikely a bug since no one else has reported anything like that.