I have a unique problem, for which I am unable to find the reason and thus not an inch closer to solution since 4 days.
Drush is taking a separate settings.php file instead of the correct one.
Check only the settings files link found on the link marked  in both the settings.
So in dev environment, drush takes the following config:
[vagrant@frontier www]$ php ../bin/drush.php core-config Enter a number to choose which file to edit.  : Cancel -- PHP ini files --  : /etc/php.ini -- Drupal --  : /var/www/sites/$DRUPAL_ROOT/cnf/settings.php  : /var/www/sites/$DRUPAL_ROOT/www/.htaccess
But on the deployment server, drush takes up the following config:
/var/www/frontier/www devtools(pabetadfsp01p):php ../bin/drush.php core-config Enter a number to choose which file to edit.  : Cancel -- PHP ini files --  : /etc/php.ini -- Drupal --  : /var/www/$DRUPAL_ROOT/www/sites/www/settings.php  : /var/www/$DRUPAL_ROOT/www/.htaccess
Now, I create a symlink at
$DRUPAL_ROOT/www/sites/default/settings.php which refers to
$DRUPAL_ROOT/cnf/settings.php. So drupal picks up the correct settings while drush doesn't.
I really don't have any idea as to what could cause this mis-configuration. Please let me know any remedy.
Also I don't create a
www folder in the sites folder at
$DRUPAL_ROOT/www/sites/ which is displayed on drush settings on deployment server.