@resoft11
Code: 
MISSING:
alteration who need to be done at index.php
$downloads = Core::load()->mapRequest('Downloads', array('page', 'query', 'type', 'site'));  <- site on array
echo $downloads->pages(array(
            array('default', WCDDL_PAGES_DEFAULT),
            array('query', WCDDL_PAGES_QUERY),
            array('type', WCDDL_PAGES_TYPE),
            array(array('query', 'type'), WCDDL_PAGES_QUERY_TYPE),
            array('site', WCDDL_PAGES_SITE)  <------------------------------------------------------ site to pagination
        ));
if uses the noxxx mod change one line
if((empty($type) && !isset($_GET['q']) && !isset($_GET['page']) && !isset($_GET['site'])) || (!isset($_GET['site']) && isset($_GET['page']) && $this->dontshow && $type != 'xxx')) {
(code from jomasaco)

Jomasaco released a module of that. I believe it's called "wcddl_joma_site_downl.php"
It will show site page with a working pagination.

The module can be found on WCDDL skins forum
Can't find the link on KWWHunction anymore.

btw you shouldn't edit the wc3.php as it will make it harder to update wcddl script in the future. Best way is to use the module.