I wanted to revisit this since it appears to still be a problem with 1.99 out of the box versions.
In addition to the code changes mentioned above one might also choose to edit around line 71:
$object->set_hidden(0, true);
AND MAKE IT:
$object->set_hidden(0);
This will prevent showing a category total and having any purposely hidden items from automatically being displayed.
Gradebook
Hiding course total without hiding entire user report
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