Ragnar,
we are on Moodle 2.9.4 and seem to have this problem as well. I suspect that what you describe about how to correct it might have something to do with the actual cause as that is really the only thing our teacher in question is doing. She unhides the topic section when the class has progressed to that point. She never grades the assignments via the gradebook, so it's really odd that they get hidden. They also don't hide anywhere else but the gradebook. Other courses that are setup the same but instead use conditional access for opening/closing topic sections, don't have this problem.
Your fix for it didn't work for me, but going into the Gradebook > category items > hiding, then unhiding the assignments did fix it.
although I really find it hard to see a connection, It could be some kind of misread for the gradebook when you unhide items that were previously hidden using the topic section show/hide toggle. Another possibility is the items were "double hidden" by using the hide on the activity, as well as the topic section and the gradebook doesn't adhere to both "unhides"
Would be nice to know what causes this but if anybody else has the problem you could try both what Ragnar and I suggested.
