Further experimentation shows Quicken 2012 will run as long as graphics --> Allow the window manager to control the windows is unchecked. A virtual desktop is not required, however the application is better suited to running with "control the windows" and "virtual desktop" checked, since it allows the user to drag the app onto any desktop. May be an issue between Quicken and the window manager (tested with XFCE and E17, not gnome or kde).
