Pretty URLs problem on custom server. Revrite_mod is in phpinfo loaded modules.

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I've a website running on a custom server, it is (Apache/2.2.16 (Debian)) with PHP Version 5.3.3-7 intalled. If I enable Pretty URLs main page is working fine but if I try to go to any other page(i.e.www.www.mydomain.com/about-me/)... I get the 404 Not Found error. What is funny if I type inwww.www.mydomain.com/index.php/about-me/... page loads normally.

Aditionally my domain points directly to the concrete root directory so my config/site.php looks like this:

...
define('BASE_URL', 'http://www.mydomain.com');
define('DIR_REL', '');
...

and htaccess file is:

<IfModule mod_rewrite.c>
RewriteEngine On
RewriteBase /
RewriteCond %{REQUEST_FILENAME} !-f
RewriteCond %{REQUEST_FILENAME} !-d
RewriteRule ^(.*)$ index.php/$1 [L]
</IfModule>

also, from phpinfo:
DOCUMENT_ROOT /home/my_domain/public_html/my_domain