I think Lynette wants to change to order of the colours within each bar ... so the light blue is not always at the bottom.
It reminds me of getting a table to sort each pane independently (I couldn't locate the post) ... but I don't think I have ever seen it applied to a stacked bar chart.
Maybe a heat map will help you visualize this better than a stacked bar chart?
Did any of these suggestions work? If not post a workbook and we can have a look at it.