Our computer services installed a development moodle server for us to test and one of these gradebook issues were there except may be for the sub categories aggregation. however, when they upgraded the production server, all these issues suddenly showed up and it is the grades submission season. Since I'm the gradebook expert in my team, I had to deal with flooding complaints about these issue.
My quick fix was to:
1. export the grades into an excel sheet
2. delete the existing grades items in moodle
3. recreate these item and categories
4. Import the grades back.
This approach, even though it is very time consuming, but it made gradebook for the courses work again.
The problem seems to be with gradebooks that were created before the upgrade (we were using moodle 2.6.2).
the reason that made me recreate these items is that in our moodle 2.8.3 installation, grade items and categories that had a maximum grade different than 100, the gradebook was still calculating them as out of a 100.
I also noticed the "natural" method is not really summing the grades. It is still using the weighting method, but uses the maximum grades for the grades items as weights adjusted to 100.