When enabling Clean URLs, test passes, but ticking & updating fails
This has taken me a long time to resolve also. You need to set the relevant line in /sites/default/settings.php to

$GLOBALS['conf']['clean_url'] = 1;


Mine was set to zero. When I updated this, I realized that my server account didn't have permissions to change the settings.php file, and I suspect this is why it was not able to be updated by Drupal.

Hope this helps