I found this in one of our courses that has no sub-categories within the gradebook and only 1 of the activities is hidden via the gradebook.
I tried very hard to determine what the teacher had done (changed a total or a weighting, overridden the total, changed the grade type to 'None' etc) but couldn't see anything wrong.
I did figure out (from playing about) that if I locked the total it displayed for the student, this was OK but we did have to remember to unlock the total before altering one of the grades which was a pain!
We're on version Moodle 1.9.10 (Build: 20101026)
I'm not sure if that helps...