problem with .htaccess file in godaddy subdomain

[eluser]psychoder[/eluser]
i have a website built using CodeIgniter with Modular extension... and htaccess to eliminate index.php in the url... now the problem is it won't work at a subdomain, but in a folder inside the domain it works...how would i figure out the correct .htaccess file..

Code:

Options +FollowSymLinks
<IfModule mod_rewrite.c>
RewriteEngine On

<Files .*>
Order Deny,Allow
Deny From All
</Files>

RewriteCond %{REQUEST_FILENAME} !-f
RewriteCond %{REQUEST_FILENAME} !-d

RewriteRule .* index.php/$0 [L]
</IfModule>
Options -Indexes