Story View showing Scenes in Reverse Order

The order in Story View is not connected to the order of navigation. It is merely SL's attempt to make a visual representation of how the triggers connect the slides and scenes. The learner never sees it.

What matters is the triggers that connect the slides or scenes to each other ("Jump to ...").  Not that it matters, but the only way you can change the order you see in Story View is by changing the jump triggers. Again, it really doesn't matter, because what you see doesn't affect, nor represent what the learner sees. It is helpful if you look at the little red lines, because they show where the jump triggers come from, and where they go.

In Story View, under the HOME tab, there is an icon to change the index number of a scene. There is another one to change which scene is the starting scene, but it sounds like you are happy starting with #1, so you probably shouldn't mess with that.

Generally, if you have one slide or scene that jumps to several others, they will show in the order of creation. However, if you look at the attached sample, you will find them lined up from left to right, which is the order the triggers that jump to them was created. The triggers are attached to shapes, and the system assumes that the shape (and the trigger that is attached to it) that is lowest on the timeline was created first, so it's scene is on the left. If you change the order of the shapes on the timeline (and therefore their triggers), you can change the order of the scenes.