index.php in sub domain not working

I have created a sub domain new.mysite.com. I have a fully functioning EE website on mysite.com and I am a copy to new.mystie.com to work on it. It moved over fine, except that all the links are broken. On the main site I remove the .index.php with the .htaccess

RewriteEngine On

    # Removes index.php from ExpressionEngine URLs
    RewriteCond $1 !\.(gif|jpe?g|png)$ [NC]
    RewriteCond %{REQUEST_FILENAME} !-f
    RewriteCond %{REQUEST_FILENAME} !-d
    RewriteRule ^(.*)$ /index.php/$1 [L]

however on the sub domain if I put the index.php in the url it works. Is there something special need to do make it work on the sub domain and still keep the index.php removed?

I looked and all the setting are the same.