This is originally reported by Stanford (CW-2340).
Here is how to reproduce it:
1. Create an assessment with "Grades sent to Gradebook" and "Automatic Submission" on.
2. Take it as a student but don't submit it.
3. Run the auto-submit Quartz job after the due date.
4. After the job is done, the submission is seen inside Sagmio but not Gradebook.