Not sure if this will help or not, but when we migrated from 1.8 to 1.9, I noticed this as well, and then went into some courses and found that the overall course aggregation method seemed to be set at "Mean of weighted grades" or something like that which gave nothing in the course totals column. But when I changed that to Simple Mean of weighted grades or Mean of Grades, then the totals showed up. So it was just a matter of changed that aggregation method.
This can also be done in the administration panel for grades sitewide- but the thing is, there's a "force" checkbox, which means that you can force everyone to use the same setting (and they have no choice). Then there's a pulldown menu for choosing one method, and my hope is that this then becomes the "default" aggregation method across the site for those who haven't made an aggregation choice yet, but I can't confirm this for sure. What I wanted to do was make Simple weighted or mean of grades the default so that people who had no clue about the aggregation method would still see something in the course total column, without forcing everyone to use the same method. I'm still not sure if setting these settings does that or if it needs to be done in code.