So what you see in Story view is SL’s best attempt to create a visual of how the course flows. Neither it nor the menu have any real relationship to how the learner will progress through the course. What controls the sequence of slides in the course is the jump triggers, If you jump to Next, moving the slide thumbnails will change the order. If your triggers jump to a specific slide, you cannot change the order or position of the slides in Story view. If you drag one, you can change its number, but not its location in the sequence. If you change to jumping to Next, any movement will change the slide order. That means that if the mouse twitches even a little bit while you are clicking the slide thumbnail, it can change its position. That’s why I always jump to a specific slide.
In short, stop “fixing” it. When you preview it, if the slides progress in the order you want, all is well. If you want to change the order, change the “jump to” triggers. You can safely ignore what you see in story view. One example may help you here: If you have a slide that has one trigger to advance, the target slide will be under and lined up with the source slide. On the other hand, if you have a slide from which a learner can advance to several other slides (like a menu slide), in Story view, the menu (source) will be on top, and the other slides (targets) will be lined up evenly under it. Story view is SL’s attempt to help you visualize, but in reality doesn’t control anything. The lines illustrate where the triggers send the flow, but don’t control it.