For each competency who have to select the which Scale to use. Then you must Configure scales to select the default proficiency values. Note: I have custom scales.
The Competency is then linked to the course and to the Course activity that awards the competency.
The Course Activity: Competencies section - the course competencies and Upon Activity completion must be populated.
the Upon Activity completion = Complete the competency.
1. If all of those settings are in place, check the course activity report. Have student's successfully completed that activity?
2. Does the Competency Breakdown Report update correctly for the Student's who have completed that activity?
3. Is your CRON jobs running for Complete learning plans which are due, Completion mark as started and Calculate regular completion data?
Once a proficiency is not working as expected, it has been my experience that I needed to manually correct it for each student.
It is a best practice, when setting up a course, to review the student experience (course navigation/quiz activity) and then review the Admin/Instructor experience (reports and learning plans) before I release it for the intended audience. Using this process, I do not need to adjust manually a large population of student's course, quiz or competency values.
Good Luck.