This happens because the Leave Feedback function in the assignment submission folder has an area where the topic’s score can be entered for that specific user’s submission. If that assignment submission folder is linked to a grade item, when any feedback is submitted within the Leave Feedback area, the feedback will overwrite any previously existing feedback or grades for that item in the gradebook.
In order to avoid this issue, enter grades from within the Leave Feedback area for each submission rather than updating in Grades directly.
Another alternative is to enter all feedback from within the Leave Feedback area, save it, and then enter grades for the item in the gradebook.