I'm sorry I have more questions than answers right now. Is this happening across all your courses? I am unfamiliar with any bug that would cause this. About the only thing I could suggest as a possible cause for this would be if the grades in the grader report were all overridden (cells would be two-toned brownish/orangish pukey color). In that case resaving wouldn't affect anything. Have you tried doing a resave for one assignment and see if that corrects the problem (perhaps on your test server, backup and restore a bad course)?
Anyone made a query to write grades to gradebook?
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