One limitation of Combine Windows is that it only creates VSplitter / HSplitter layouts, and does not have an option to tab the reports during combining. So I am guessing that you rearranged the running dashboard to create the layout in the first picture? What you are seeing is that changing the layout of a running dashboard currently does not change the dashboard script. If you change the layout in the Dashboard Builder (either create directly in Dashboard Builder, or Combine Windows and then red-triangle > Edit Dashboard), then you can save from there and the layout will be preserved.