When CiviCRM is installed to DRUPAL_HOME/sites/all/modules/civicrm, resource URLs are generated correctly. However, when it's installed to DRUPAL_HOME/sites/<site-name>/modules/civicrm, resource URLs are not correct and manual intervention is required to set the to proper value.
During CRM_Core_Config* refactoring, I came over the part of code that is responsible for this and added quick "stub" with FIXMEs. It can be found in CRM_Core_Config_Default:145. The stub handles single case when Drupal site is called "trunk" (which is my developer sandbox address).