Why is mod_rewrite only working for one virtual host but not other?

I have two applications running on the same droplet (Ubuntu 14.04, Apache 2, PHP 5.5.9) each one as a different virtual host.

On application is using Codeigniter 2.2.6, the other one Codeigniter 3.0.6.

Both applications have very similar Apache .conf, .htacces files, where the only difference is the domain name.

Also regarding Codeginiter, both have very similar config files with $config[‘index_page’] set to empty.

My problem is that mod_rewrite is only working for the oldest application running Codeingniter 2, and not for the new one in Codeigniter 3.

Locally mod_rewrite works fine on both apps under MAMP.

Any ideas of what could be wrong?

.htaccess

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

<IfModule !mod_rewrite.c>
	ErrorDocument 404 /index.php
</IfModule>

.conf

<VirtualHost *:80>
        <Directory /var/www/>
                Options Indexes FollowSymLinks MultiViews
                AllowOverride All
                Order allow,deny
                allow from all
        </Directory>
        ErrorLog ${APACHE_LOG_DIR}/error.log
        CustomLog ${APACHE_LOG_DIR}/access.log combined
</VirtualHost>