Is the Competencies linked to a Learning Plan template? Is the learning plan template assigned to students as a Learning Plan?
Does the course completion reports display that the Student completed the course and all activities?
Is your Cron job running for course completion? My Moodle is set at every 1.
Did you setup the competencies and course relations for a course that was completed in the past? (competencies are not awarded to completions in the past).