CodeIgniter site in subdirectory, htaccess file maybe interfering with htaccess file in main directory?
The CI .htaccess shouldn't be in the application folder; it should be in the root of theSubDomain folder. e.g. /public_html/SubDomain/.htaccess
Also, in that .htaccess, you need to set the RewriteBase:
<IfModule mod_rewrite.c> Options +FollowSymLinks RewriteEngine on RewriteBase /SubDomain RewriteCond %{REQUEST_FILENAME} !-f RewriteCond %{REQUEST_FILENAME} !-d RewriteRule ^(.*)$ index.php?$1 [L]</IfModule>