After migrating some Joomla-sites from an old server to my new webserver with suPHP the search engine friendly urls didn’t work anymore.
The main problem was that the layout was disappeared for all sites other than the main site.
In the source code of such a page I found that all CSS files had a wrong referral url:
The starting “/index.php” should not be there.
Also in other links in these page a “/index.php” too much is in the links.
The issue was solved by entering a value for the variable
var $live_site = '';
in the configuration.php:
var $live_site = 'http://www.example.com/joomla';
The Joomla pages all had version 1.5x.