Alexander Kops

I have the same problem. I solved it by altering the ksuce_exclude_categories-function to preserve the “category__not_in” settings in the query, if there are any, and just add the blocked ones:

function ksuce_exclude_categories($query) {
    $options = ksuce_get_options();
    //Mod: Do not override existing excluded categories
    $categories = $query->get('category__not_in');
    $array2 = empty($categories) ? array() : $categories;
    if ($query->is_home) {
        foreach ($options['exclude_main'] as $value) {
            $array2[] = $value;
        }
    }
    if ($query->is_feed) {
        foreach ($options['exclude_feed'] as $value) {
            $array2[] = $value;
        }
    }
    if ($query->is_archive) {
        if (!is_admin()) {
            foreach ($options['exclude_archives'] as $value) {
                $array2[] = $value;
            }
        }
    }
    $query->set('category__not_in', array_unique($array2));
    //Mod end
    return $query;
}

So now when you use
query_posts(array('category__not_in' => array(1,2,3));
and have blocked the category ids 3,4,5 with the plugin, it will ultimately block categories 1,2,3,4,5