Clean URLs aren't being displayed I want clean URLs like webpage.com/page instead of webpage.com/?q=page, specifically in my menus.

I have gone here http://v6.dev/admin/config/search/clean-urls (which is a clean URL and works) and ticked the 'enable clean URLs' option and saved. But nothing happens, the page reloads without the tickbox checked.

Clean URLs are working, I can navigate to webpage.com/page fine, but the menus aren't being generated as clean URLs.

I have gone through this page: https://www.drupal.org/getting-started/clean-urls but can't solve the problem. I think the servers set up okay, because I can succesfully navigate to clean URLs, it's just that links aren't rendered as clean URLs.
I've also tried cleaning the cache, and restarting server.

If it helps, I'm generating menus with this code:

&lt;?php
    $menu = menu_navigation_links('menu-top-menu');
    print theme('links__menu_main_page', array('links' =&gt; $menu));
?&gt;
First thing I would check is the .htaccess is indeed working...maybe your getting a cached version of:

http://v6.dev/admin/config/search/clean-urls 

What happens when you enter a URI which you know has never existed (and been cached) such as:

http://v6.dev/xxx-237347-3iu33

Does it 404? Does drupal handle it and say "page cannot be found"?

I had a similar issue a few days back...I had to manually disable "clean uri's" in the database...flush all cache tables...re-enable mod_rewrite...log in and enable clean URI's

Let me know how you turn out. :)