With customised Columns, Burndown Charts and other Reports ignore Resolved Issues

I have an Agile Scrum Board with multiple Projects.

I just split the Done column into separate Resolved and Closed columns, and I mapped the Issue Statuses accordingly. I did not change the Workflow or add new Statuses or anything. I have been prompted to re-index twice in the last week (and have done so), so this could also be related to that.

Quite unexpectedly, all the Charts in the Reports section are broken. All Reports display data as though none of my Issues have been Resolved or Closed. Further, the Plan view shows Resolved and Closed issues in the Backlog (correctly crossed out, but they should not appear at all).

The Issue data is correct, it just seems as though JIRA Agile is not properly displaying the Issues. Is this something I've done? Could this have been caused by an OnDemand update in the last week? Is there a way I can fix my JIRA Agile?

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The Done status is special. It comes with JIRA Agile and I don't recommend changing its name or trying to divide it's purpose into two parts. Stick with one "Done" status to be safe.

I expect the name "Done" is hard coded into the reports. I'm confident that the column position has very little to do with the reports working correctly.

Is this a known issue with JIRA Agile? Is it worth reporting this as a bug or feature request? Reports really should be based on Issue Status, it seems counter-intuitive to have them depend on the names of Agile Columns.

To me, the Agile Columns are for visualising and transitioning Issues through a Workflow. In MVC terminology, the Issues are the model and Agile Columns are a view/controller. Agile Columns should never be used as a model.

I reversed my changes to the Board's Column Layout and Issues Status mapping, and everything is functioning as expected again. I consider this an interim work-around, as the Reports and Plan views really should be based on Issue Status, not Column Layout.

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