The way slides appear in the Scenes panel (as well as in STORY VIEW) is based on the programming.
Slides within a scene will appear in a vertical stack when they are connected linearly by triggers. Typically, that connection is done with the Next button, which has a trigger that jumps to the "next" slide in the sequence within a scene.
When a slide isn't linked to the slide with the previous sequence number, it appears in another stack.
When one slide links to multiple slides, the program tries to represent the branching using multiple stacks.
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The way slides appear in the Scenes panel (as well as in STORY VIEW) is based on the programming.