Hi David,
I already get the same kind of problem than you. The second application in your Windows taskBar is not a second instance of your application but comes from the panel currently displayed. Which means that somewhere in your uir file, you must unchecked the "Has TaskBar Button". Go in your uir file, double click on your panel, click on "Other Attributes...", it should be there. This option creates a specific instance for the panel (don't ask me the utility of such an option - yet, there must be one...)
Hope this helps; good luck.
Flo.