If anything that is drawn there stays there until overwritten.
Try setting a wallpaper.I think the gnome way of doing it is launching system settings and clicking on appearance.
Cannot say for sure whether or not a program needs to actively tend to the root window, or if there's some X11 flag to clear the drawn pixels of off any window automatically as it is deleted.
I've always solved this issue with setting a wallpaper or a solid color.
