I have closed JIRA's in the To Do column that I would have thought should be in the Done column. The JIRA's do have a Closed Sub-Task attached. Is this reporting correctly?

[Steve Behnke [DiscoverEquip.com]]

Could it be that that the Sub-Tasks are 'Closed' but the Story is still 'Open?' If you want this to automatically close out when all Sub-Tasks are complete you'd have to implement this in your workflow. 

[Nic Brough -Adaptavist-]

Check the board definition - what status exactly do you have in the To Do and Done columns?  Now look at the plain issue view of an issue you think is wrong - what status is that in?  If that is mismatched, could you try re-indexing the project and see if that helps?

[Phill Fox]

In addition from the comments from @Nic Brough [Adaptavist] you should check that you are not confusing resolution with status. A resolution can be set independent of the status. If an issue is set with a resolution but then moved back in to the "To Do" column it may not have had the resolution cleared and this show as a crossed our number. The fix for this is to 1. Amend the workflow so any move away from Closed resets the resolution to empty. 2. For all items not in Closed do a bulk fix to reset the resolution to empty.