I did a manual installation of eZ and chose the host access mode by using

[SiteAccessSettings]
MatchOrder=host

in settings/override/site.ini.append.php

When viewing the site all links include "index.php". This should not happen in virtual host mode, right?

When I force virtual host mode by using

[SiteAccessSettings]
ForceVirtualHost=true

in settings/site.ini no index.php is included in the links.

So the virtual host mode is not being detected automatically as it should. I can not provide more information right now, because I don't know what tests are run by eZ to see if it is in virtual host mode or not. Is there anything you need to know to see if this is a bug or a configuration issue?