Civimail & Drupal Multisite -- tracking url looks in wrong location for civicrm.settings.php
KEY thing is that when you have a Drupal multi site config - make sure that each civicrm is in its corresponding /sites/example.com/modules

You can structure that too: put your CiviCRM versions in one central place eg /var/www/ so you have a civicrm/4.6 a civicrm/4.7 etc - then add a symbolic link in each projects /modules directory to the /var/www/civicrm/4.x version it's on.

This way you can now easily update both minor Drupal and minor CiviCRM versions across all your sites/projects!

EDIT: example:
in /home/karin/org.ca/modules


  lrwxrwxrwx.  1 karin karin    20 Jan 15 13:37 civicrm ->
  /var/www/civicrm/4.6