Okie, kuroi, so I went ahead and made the changes, and it seems to work pretty well, here is what I do:

First, Go to the admin/includes/boxes, assuming all the files there are the original ones:
I overwrite configuration_dhtml.php using your file.
For the rest, I search for:
PHP Code:
$za_dir->close();
} 
And add below:
PHP Code:
foreach ($za_contents as $key => $value) {
    if (page_allowed($value['link'])!='true') unset($za_contents[$key]);
} 
Now I edit admin/includes/functions/admin_profiles.php

I search for:
PHP Code:
$page = strip_suffix($page,".php"); 
Add right above it:
PHP Code:
if(strpos($page, HTTP_SERVER) !== false || strpos($page, HTTPS_SERVER) !== false){
        $page = current(explode('?', end(explode('/', $page))));
    } 
Done!