Udo ~
it looks very much like the rewrite engine doesn't find index.php and
thus rewrites the URL to that of a wiki page called "index.php".
A new suggestion to solve this: Add a RewriteBase clause to
your .htaccess, like this:
htaccess in /wiki:
RewriteEngine On
RewriteBase /wiki/
RewriteCond %{REQUEST_FILENAME} !-f
RewriteCond %{REQUEST_FILENAME} !-d
RewriteRule ^(.+)$ index.php?title=$1 [L,QSA]
~ Kilian