clean urls - site links missing {shortname} in url

hey there,

i believe i have multsite_manager setup properly using clean urls, and it does seem to work, however when you goto one of the sub-sites - all the links are missing the {shortname} that is specified... rendering the primary links URL in the format of /site/forum instead of /site/wap/forum

so again to review, i am able to to goto *.com/site/wap/ but then all the links are ending up *.com/site/forum instead of *.com/site/wap/forum which im guessing should be the intended operation

My .htaccess due to clean url's being used

RewriteEngine on

#file access
RewriteRule ^\w+/(modules|misc|files|themes|sites)(.*)$ ./$1$2 [L]

RewriteRule ^/(modules|misc|files|themes|sites)(.*)$ ./$1$2 [L]

#special php scripts
RewriteRule ^\w+/(update.php|install.php|index.php)(.*)$ ./$1$2 [L,QSA]

#site sub-section
RewriteCond %{REQUEST_FILENAME} ^/home/user/public_html/thewebsite.com/site/.*
RewriteCond %{REQUEST_FILENAME} !-f
RewriteCond %{REQUEST_FILENAME} !-d
RewriteRule ^\w+(/)?(.*)$ index.php?q=$2 [L,QSA]

#### clean url stuff should be further down in default file

replacing the /user/ and /thewebsite.com/ with the particular specific information

and then my settings.php which is locate in /sites/wap.thewebsite.com/settings.php

$matches = FALSE;
if (preg_match("|thewebsite.com|",$_SERVER["HTTP_HOST"])
    && preg_match("|^/site/(\w+)|",request_uri(), $matches)
    && $matches)
{
  $my_site_base = $matches[1];
  $db_prefix = "". $my_site_base ."_";
  $base_url = "http://thewebsite.com/site/". $my_site_base ."";  // NO trailing slash!
  $db_url = "mysql://DBuser:DBpassword@localhost/actual_database";
  $db_prefix = '';
  ///This assumes you have a ./files directory in your base drupal directory
  $conf = array(
        "file_directory_path" => "files/".$my_site_base,
  );
}

ive done a bit of research and testing, it doesnt seem like im doing anything wrong, but i could be wrong on that notion as well. the database for the new multisite does get created and seems to be populated. could it be a setting in the database causing it? i dont know, im kinda lost as to where to start with resolving this...

any suggestions would be much appreciated