I've seen this happen too. While I was unable to determine why the overrides were happening, if you install LAE grader report https://moodle.org/plugins/gradereport_laegrader it will allow you to have a button at the top of all columns in the gradebook and simply click the button to remove all overrides.
I know that doesn't exactly solve the problem but it's the workaround I've been using. Hope it helps!