Comment 22 for bug 1059374

Adding this to gtk-widgets.css will "fix" it for Numix and whatever other themes are spawned from it:

GtkWindow {
    color: @fg_color;
    background-color: @bg_color;
}
GtkPaned {
    background-color: @bg_color;
}
GtkEventBox {
    background-color: @bg_color;
}

However, this workaround does not work for Zukitwo, for example. Disabling overlay scrollbars most certainly is not "a solution".