Problem with base_url()

could you elaborate the changes that you made in the .htaccess file?

If with index.php it's working, I believe the problem is in htacess.

You can try this rewrite code on you .htaccess.

Code:

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