aakk9999 - 12:07 pm on Feb 20, 2011 (gmt 0)
I am using this piece of htaccess code to rewrite / to /index.php
Perhaps the problem is in terminology you are using in this sentence. You do not have to use rewrite to rewrite / to index.php providing that index.php is a default page that is returned when the root is requested.
What you need to do is have a 301 REDIRECT that redirects all external requests for /index.php back to root / I think the .htaccess code TheMadScientist gave you in your message above does this job now.
Internally, you have to link to / (and not to /index.php) so that there is no internal redirect performed. You can use Xenu Link Sleuth to check your site to ensure there are no internal linking to /index.php