Problem with links

I had some issues with installing the blog on brinkster, finally solved it by commenting some lines and updating the wp-settings.php file.

Now some of links for Pages and Categories seem to be invalid.

the link shows http://natureisbeautiful.vividscapes.com/?cat=5
instead of the correct one including the index.php?

here is the link to my previous post – http://wordpress.org/support/topic/184842?replies=5

is there a table or config file where i can hardcode the folder path for it to work correctly.