Usually the Tax not Included will show up because someone adjusts the tax by using the magnifying glass button at the bottom beside the taxes. When an adjustment is done through this dialog, the program understands that the total tax is the amount listed but some of it is not included in the line items. So it is marked as such. If you want to adjust the tax and show it as one total, do it on each line item applicable. Use the menu option Sales, Tax Summary for Line or Ctrl-Y when your cursor is on the line.
Hope this was the answer.