There is a minor bug in block_settings_renderer::settings_tree, when it is counting the children it doesn't exclude hidden items.
If you have the "My profile settings" item hidden, for example, it will still show a hr before "Site Administration", when it shouldn't.

The fix would be to change:

foreach ($navigation->children as &$child) {

    $child->preceedwithhr = ($count!==0);

    $count++;

}

To:

foreach ($navigation->children as &$child) {

    $child->preceedwithhr = ($count!==0);

    if ($child->display) {

        $count++;

    }

}