Gradebook

Actually, I think I managed to pinpoint the problem with extra credit. On the test site, one of the parent categories had "Aggregate including subcategories" ticked. This changes how aggregations and totals are calculated quite a bit. Unless you are confident with how this works, it would be better to always leave this option unchecked. This is what I've done with the categories you were showing in your screenshots, and now the totals display normally.