We have experienced this same issue recently. It may have only occurred since we upgraded to v2.9 but I cannot say that with 100% certainty.
In our case, it affected a user in an old course that has been used since 2011. Three quiz results the user had received grades for are not appearing in the Gradebook (grader report) or the User report.
Unfortunately, I can't confirm if the grades were ever present in the Gradebook but I can say that some quiz questions were edited in 2 of the quizzes and quiz settings were updated in the other quiz AFTER those attempt were submitted.
We are using the override option in the Gradebook to correct the problem rather than regrading the attempts.