So I found that my footer menu links were respecting the "paramaters - system" > "SSL Enabled" being set to checked or unchecked.
Well that pointed to mod_roknavmenu as the reason why ssl links weren't being set as such, and sure enough I found it to be the case since the default joomla menu module and mod_roknavmenu varied in the following:
See /modules/mod_roknavmenu/lib/RokNavMenuTree.php , on or around line 312 - in the following (the last "else" block code is the fixed version)
if ($tmp->type != 'separator' && $tmp->type != 'url') {
$iSecure = $iParams->get('secure', 0);
if ($this->_params->get('url_type','relative') == 'full') {
$tmp->url = RokNavMenuTree::_getSecureUrl(JRoute::_($tmp->url, true, $iSecure),$iSecure);
} else {
$tmp->url = JRoute::_($tmp->url, true, $iSecure);//Added 2nd and 3rd argument - copied from the default joomla menu module
}
}
The "else" was not passing the 2nd/3rd arguments to JRoute::_, so it just did the default (if your site is set in the global config to force SSL, it would be SSL, and if not, it wouldn't be). This was a problem for an ecommerce site since we only want the checkout to be secure to speed things up.
In Summary: Go to line 312 and replace $tmp->url = JRoute::_($tmp->url); with $tmp->url = JRoute::_($tmp->url, true, $iSecure);