php_value allow_call_time_pass_reference 0
<FilesMatch ".">
order allow,deny
allow from all
</FilesMatch>
<FilesMatch "(index\.php|\.(gif|jpe?g|png|css|js|html|avi|mp3|swf|flv|cur|ani|php|kml|xml|wmv)|var(.+)storage.pdf(.+)\.pdf)$">
order allow,deny
allow from all
</FilesMatch>
RewriteEngine On
RewriteRule content/treemenu/?$ index_treemenu.php
RewriteRule index_treemenu.php - [L]
RewriteRule !\.(gif|jpe?g|png|css|js|html|avi|mp3|swf|flv|cur|ani|php|kml|xml|wmv)|var(.+)storage.pdf(.+)\.pdf$ index.php
DirectoryIndex index.php
the reason is that you have added an very optimistic match for avi files (and many others).
I don't use .htaccess my self, so not sure what is best but it makes apache try to serve the file, and when you add index.php, eZ Publish does not recognize index.php as a module (read the error). Just try changeing the file type to make sure it falls true the rewrite rules correclty: