I have faced this problem many times, so thought this could help the person reading this 🙂
 Often in Dupal 7  when you go to Configuration>>Clean URLs and “Run the clean URL test” it will give a failed run message even though the server have the capability to have clean URLs.
In this case all you have to do is to replace the clean URLs link on the browser from      

“http://www,yourdomain.com/?q=admin/config/search/clean-urls”
                          TO  
“http://www,yourdomain.com/admin/config/search/clean-urls” and enable Clean URLs.

Hope you now have the Clean URLs on your site!!