Indeed, sub-menu items in the current Superfish version are sorted according to the order they have been created.
There’s an issue regarding the enabled/disabled state with the currently latest stable version (8.x–1.0-rc2) of the Superfish module which the theme uses for its multi-level menu.
Workaround
In order to bypass this one can edit existing menu items to display the links in the position they want or add new items and delete the old ones.
This issue remains in the current dev version of Superfish, so the workaround discussed above, would be your best option at the moment.