Comments and Pages don’t work

On my hosted site the new url format for Comments and Pages does not work. The new link form is like http://host/Blog/?page_id=7 while the old (v1.3) form was like
http://host/Blog/index.php?page_id=7. With the new form, all links which start with the ‘?’ redirect to index.php. For comments the change is similar. Now it is
http://Blog/?p=20#comments and this redirects to index.php. If you type in
http://host/Blog/index.php?p=20#comments you get the correct page. The new form works on my localhost, so it is a problem with the host somehow and the way virtual hosts are setup. Everything would work if I could get the WordPress links to include the index.php prefix. Does anyone know how to change wordperss to do this?