Can't save Drupal role permissions for CiviCRM
Will permissions for non-civicrm related permissions "stick"? If not I've seen this problem before when there are too many roles/permissions on the form. Drupal commons installs a lot of modules, so its possible. You should either edit permissions for the roles individually, so for authenticated user for instance goto admin/people/permissions/2

I believe its the php.ini environmental variable max_input_vars and you should increase the number to get the full permissions form to work