Your question is from 2016, but alas... others might come looking for an answer too.
When you "order by status" in a JQL or use Status in dashboard gadgets, they are ordered according to that global order you captured.
Generally you'd like to have all "todo" statuses on top of that list, "in progress" in the middle and "done" statuses by the bottom.
If you run a simple jql: "order by status asc" and think some issues should appear on top of others, it's likely you'll have to move statuses up or down in that administration screen.
I have multiple projects that use variations of the same base workflow. The variations depend on the requirements of the project or issue type. The variations mostly come in the form of new statuses ...
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