We had a problem with a promo tool that uses rewrites in .htaccess subdirectories.
Maybe, this might help ...
Code:
Note: There may be a long file like httpd.conf that may contain your domain's configuration.
Edit your domain configuration;
pico /etc/apache2/sites-available/doc_root
Set the Overide for your domain configuration
Paste with your path;
<Directory "/home/user_name/www/public_html/domain">
AllowOverride All
</Directory>
Then;
Cntl+X
Y
enterkey
Then restart the Apache server
This was part of the manual fix instructions I did.