@aschuler when you launch Sublime Text from the command line, Gnome Shell doesn’t know what icon
it should use for the window so it uses whatever the application provides as an X11 property (_NET_WM_ICON).
I presume ST2 sets the proptery implicitly through GTK2, so it’s going to be tough to build a workaround.
Gnome Shell does have a JavaScript API though, you could try that.