Drush does not download modules correctly Drush says it downloads a module successfully but instead of putting it in sites/all/modules it puts it in the current directory:
$ drush dl module_filter
Project module_filter (7.x-2.0-alpha2) downloaded to                 [success]
/drupal/module_filter.
The folder doesn't exist, but if you run the command again the following happens:
$ drush dl module_filter
Install location drupal/module_filter already exists. Do you want to overwrite it? (y/n):

drush version 7.x
Drush will put downloaded modules in the current directory if it cannot bootstrap a Drupal site.  Run drush status to determine whether or not the Drupal site you think you are operating on is recognized by Drush.  You might need to use the --uri option to specify the name of the folder that contains the settings.php file, or set up a Drush alias file.