In your CSSMenuWriter folder in the site there are two locations where the menu is stored, there is one copy for the index page and another for the content pages.
The menu on the index page is controlled with the cssmw_home > menu.php file and the content menu is controlled with the cssmw_content > menu.php file.
In here at the top of the file you will have your root values like this:
$WA_localRoot = "/sa/";
$WA_remoteRoot = "/";
This is where you need to adjust the paths. You should see one with the httpdocs in it and remove this part of the URL if it is interfering with your menu.