To more precise, pressing the Run... button in the Run Application window while Gnome is still loading its applets does not seem to refresh the window manager.
However, after waiting a few seconds for Gnome to load its applets, pressing the Run... button consistently seems to refresh the window manager.
Also, instead of actually pressing the Run... button, I also tried escaping from the Run Application window. That also seems to refresh the window manager!
To more precise, pressing the Run... button in the Run Application window while Gnome is still loading its applets does not seem to refresh the window manager.
However, after waiting a few seconds for Gnome to load its applets, pressing the Run... button consistently seems to refresh the window manager.
Also, instead of actually pressing the Run... button, I also tried escaping from the Run Application window. That also seems to refresh the window manager!