1) Gopher doesn't have any flow charts. What kind of flow charts in particular are you looking for?
2) We are working on job costing reports but they're not available yet.
3) The Gopher 2006 download doesn't affect your Gopher 2003 icon. You need to save gopher2006.exe file (from http://www.getgopher.com/2006) to your desktop in order to see a new icon. If you see "Gopher 2003" when you run the program it means you're running the older version.