If you are sending different commands to each window, what I would suggest is to try using the 'Perform a Window Function' action and change the window title of the second instance when you start it up (if it's originally titled, 'World of Warcraft', re-title it as 'World of Warcraft 2', 'World of Warcraft 3', etc.). Then, target by window title (and not by exe name) when you execute your command.
Hope that helps!