1. Go to Site administration->Grades->Grader report
2. Untick "Show only active enrolments" to disable sitewise setting
3. Create a course with assignment
4. On assignment page got to "View all submissions"
5. In separate tab go to "Grader report preferences" for your course
6. Change "Show only active enrolments" on "View all assignment page"
7. Refresh grader preferences page and observe on grader report page "Show only active enrolments" being changed
8. Similarly change "Show only active enrolments" on grader preferences page and Save changes
9. Refresh "View all submissions" page for assignment and observe Show only active enrolments" being changed

Not sure why changing one module setting affects other moodle part. May be it is desired. But it is weird way to set pref in assign module for gradebook. If it is desired - can be closed