See this video, Closing project window when maximize in Gnome Desktop cause UI problem in next project session. This doesn’t happen if Close the project window when unmaximize.
Workaround:
Open the project in other Desktop such as XFCE, unmaximize then close the windows.
Fedora 20 64-bit, Gnome shell 3.12.2, GTK 3-3.12.2-2