Change Site Url Value

I noticed that the site url in header.inc.php gets set to

$site['url']               = "http://sitename.com/folder/";  is there any reason why the www is not there

ie  $site['url']               = "http://www.sitename.com/folder/

Google analytics seems to get upset that its not

Using www. or not is debatable.

For the purposes of SEO you should decide whether you're going to use it or not and stick with your decision. In your htaccess direct non www to www (or www to non www depending on your decision) so Google sees yoursite.com and www.yoursite.com as the same address.