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