It's unable to answer your question since you haven't specified any particular information about your server configuration.
Common thoughts:
mod_negotiation has nothing to do with security: https://httpd.apache.org/docs/2.2/mod/mod_negotiation.html
So, it's just a way Apache handles requests to non-existing files. If you have this module enabled and active for the directory of Mibew Messenger it can disrupt the process of handling requests by Mibew Messenger itself.
Sorry, I didn't understand what should I do.
Here is my secure.conf:
<Directory /var/www/*>
   Options +Includes -FollowSymLinks +SymLinksIfOwnerMatch
   AllowOverride FileInfo AuthConfig Limit Indexes Options
   Order allow,deny
   Allow from all
</Directory>
<Directory /var/www/*/data/www/*/cgi-bin>
   Options -Indexes
</Directory>
<IfModule php5_module>
   php_admin_value open_basedir "."
</IfModule>
<IfModule php4_module>
   php_admin_value open_basedir "."
</IfModule>
Action php-cgi /php-bin/php
Do you you need some another information about apache configuration to find the solution for the issue?
Should I change Options at Options=All,MultiViews to make Mibew work safely?
You know, changing the secure.conf with
<Directory /var/www/*>
	Options +Includes -FollowSymLinks +SymLinksIfOwnerMatch
	AllowOverride FileInfo AuthConfig Limit Indexes Options=All,MultiViews
	Order allow,deny
	Allow from all
</Directory>and restarting the apache with
service apache2 restartdidn't change the situation
Any ideas?