Are you saying you are using the Visio Data Visualizer? This is NOT Microsoft Visio. As far as I can tell it is an Excel addin which uses some of Visio's capability to create graphics from Excel. Without a licence for the full Visio application, I don't know how much you can do to rearrange the graphic that the addin creates. Do you get any clues from sites like this?
Using the Visio Data Visualizer in Excel
Looking at your dataset, Function7, 8 and 9 all have 'Next Step ID' entries which would imply that they aren't final stages. If this data was automatically mapped as a swimlane type flowchart graphic, I would expect to see the last swimlanes containing flow end points - no more Next Steps (in your data that appears to be Function4 and 6).
I don't believe that sorting the data in Excel should have ANY effect on the arrangement of the generated graphic. Logically the resulting graphic should be considered like a 'line of best fit' whereby the graphic engine should arrange the flowchart according to the principles of:
1. Start top left and tend to flow to the right and down (like English reads on a page)
2. Minimise crossing flow lines
3. Minimise length of flow lines