htaccess for pointed domain

Hi Friends

I have registered a domain on godday and using the hosting service on other service provider. First I have transfer the domain to the hosting provider one and then pointed it to a folder. Now according to the documentation I have included the following code in my htaccess file

Code:

<IfModule mod_rewrite.c>
RewriteEngine On
RewriteBase /
RewriteCond $1 !^(index\.php|resources|robots\.txt)
RewriteCond %{REQUEST_FILENAME} !-f
RewriteCond %{REQUEST_FILENAME} !-d
RewriteRule ^(.*)$ index.php?/$1 [L,QSA]
</IfModule>

Now what I am getting is sometimes the index.php? appears on the urls and sometimes not.

pleas help if I am doing anything wrong.