Hello,
php checks are done on /var/www/html/* to see if those links exist. If the paths exist (webmail, squirrelmail, roundcube), then ones that do will show up in the skin.
If you've secured your php.ini (disable_functions, safemode, openbasedir) such that either php is not allowed to see that folder.. or the permissions on the folder are such that the DA user cannot read them, then they won't show up.
John