Have you saved the layout? (disc symbol) I mean when you leave the workflow designer ang go back, does the workflow still look the way you want it? I mean you can apply changes to the layout even if the workflow is currently in use. I just tried to reproduce your problem by changing the layout of the standard JIRA worjkflow and it just worked fine
Yes it saved, when I open the workflow with the designer tool it looks well but when I applied the workflow system and I test it in an issue, the scheme is different.
I had the same problem for my others workflows, so I tried to move transition arrows (start and end nodes) and It worked. But not for this one.
I used a trial version of Jira (4.4.4).
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