I notice that when I move a story from a backlog column, directly to done, it is not marked as resolved. (There may be other cases where this happens, it has happened with several issues).
I have a special 'Resolution fix' transition that moves an issue from Done -> Done and use the Resolve Issue Screen. I use this transition to force to mark issues, in the Done column, as resolved, but why is this happening in the first place? Is there an underlying problem that needs to be fixed?