In course/edit_form.php there is an IF statement, that displays the "cost" field only if default enrolment method is not "manual". It makes sense as the cost field is usually only used by PayPal or Authorize.net. However in some cases admins want to set the cost of the course even they have set default enrolment to "manual" - e.g. when they use "External DB enrolement" together with "Course ordering and invoicing" (http://docs.moodle.org/en/Course_ordering_and_invoicing).

At the moment there is no clean way how to force Moodle to always display course cost setting field with default enrolment plugin set to "manual". I consider this as a bug.