After updating Greenhopper to the latest version (6.1.3.1 from 6.0.2), our Agile boards are showing zero issues in the backlog. I have completed all of the troubleshooting steps documented on the Atlassian KBs for this issue to test this, including the following:
* https://answers.atlassian.com/questions/43735/issues-not-showing-up-in-plan-view-of-rapid-board
* https://confluence.atlassian.com/display/GHKB/Empty+Backlog+Even+Though+Issue+Exist
* https://confluence.atlassian.com/display/ONDEMANDKB/Backlog+is+Empty+in+The+Scrum+Board
The custom field Sprint is enabled and not hidden, the context is global and not focused to specific projects, the search context is correct, the board's filter is not filtering the issues, and all statuses that are mapped to issues we expect to see in the backlog are properly associated in Greenhopper's configuration for the columns. I do not have an epic selected in the epic selector, so it should not be filtering the board at all.
Additionally, we had not been using the classic board, so our Epics are not eligible for the migration to the new board (though I checked that to make sure).
Beyond all that, everything worked swimmingly prior to the update this morning. We were previously on the 6.0.2 release. No changes were made to our configuration aside from the update of the GreenHopper plugin from 6.0.2 to 6.1.3.1.
Unfortunately due to this, we cannot create new sprints at present, and since Monday is normally the Sprint planning session, not only was it a bad time for me to have updated the plugin (in my defense, I never expected that a plugin update would impact key functionality to this level), and unfortunately there is no supported downgrade mechanism, so we're pretty much dead in the water at this point as far as Greenhopper is concerned until we can determine why the issues that show up properly in the issue navigator are not showing up in the backlog.
Users can still work because the issues are still viewable in JIRA, but it is quite a bit impact to productivity to have to manually filter to find the issues rather than pick from the SCRUM board.
It's worth mention that the currently running Sprint itself is showing properly and all issues associated with the sprint are showing -- it's just the backlog in Plan view that is completely empty now.