When ordering the versions on the story map we respect the order you have selected in the releases tab. Due to inconsistencies in the Jira software this order is reversed in the Backlog view, this is a documented issue across Jira.
You can read more about it here, it was raised by Martin Jopson (the former product manager for Jira Software) so they are definitely aware of this shortcoming.
As soon as Atlassian releases a fix for this we will ensure we are consistent with their formatting. Until they make this consistent we have decided to base our order on the customisable order in the "Releases" tab.
To change the order they appear on the story map you can navigate to the "Releases" tab (the ship icon) and drag the releases to the desired order.