Comment 3 for bug 1268243

Ok, so I've come up with a workaround. If you add this snippet to gtk-widgets.css or some separate css file that you include in gtk.css, Synaptic will look ok. Downside is that since Synaptic doesn't set a widget-name or has a separate class, this will affect all other apps with the same widget structure...

GtkWindow > GtkVBox > GtkHandleBox,
GtkWindow > GtkVBox > GtkHandleBox > GtkHBox > GtkToolbar {
    padding: 6px;
    border-style: none;
    background-image: linear-gradient(to bottom,
                                      shade(@toolbar_bg_color, 1.0),
                                      shade(@toolbar_bg_color, 0.88)
                                      );
    box-shadow: inset 0 -1px shade(@toolbar_bg_color, 0.75);
}