This issue actually is caused by null value in "final score" column in sam_assessmentgrading_t table. That is, for any assessment with at least one student having null final score, when you edit the score in Total Score page or edit the score in Question Score page, the score will not be sent to gradebook. In Question Score page, there is even an WARNING:

Warning: A gradebook entry could not be created for this assignment. Please contact your local help desk for assistance.

To reproduce this bug, here is the steps:
1. Create an assessment and set to "Record the highest score".
2. Login as a student and submit the assessment.
3. Take the assessment again but without click on either "Save and Exit" or "Submit for Grade". You can just close the browser or log out.
4. Log in as instructor.
5. Update the score in Total Score page. Notice the score is not updated in Gradebook.
6. Update the score in Question Score page, You will get the above warning and the score is not sent to Gradebook either.