We're not using 3.1 just yet (although we're testing 3.1.3, and I cannot replicate your issue).
However, we have had similar problems in the past where staff have hidden an item in the grade book, then unhidden it, BUT they never clicked the Save changes at the bottom of the page. The item shows as visible, but for some reason this doesn't flow through to the student view. Try going back to the gradebook setup, hide the item, click Save changes. Unhide the item, click Save changes.