Arrangement/order from layout not applied

Since you didn't attach a .story file, I'm guessing that the picture is in a placeholder.

Any permanent object (e.g., a shape or photo) on a Master Layout will always appear below the placeholders (e.g., the editable boxes). That's true even if the permanent object appears above the placeholder in the Timeline on the Master.

Why? Those permanent objects aren't editable from the slide. You can't change them with a trigger on the slide. And they don't appear in the slide's Timeline. Thus, they end up below the objects that do appear on the Timeline.

To get the look you want, you could add the black rectangle on a layer on the Master. Also put a trigger on the Master that shows the layer when the timeline starts.

• Note: if the slide also has layers, you'll have to set the Slide Layer Properties to not automatically hide other layers. And, as needed, add triggers to hide layers when a user moves between layers on a slide. 

If that's not the issue, well, troubleshooting is just guessing without seeing the .story file. Here are the best practices for uploading that:

• Only include slides that are related to the problem.
• Be sure objects, layers, motion paths, and variables have meaningful names.
• If there is proprietary content, replace or delete it. For example, replace proprietary text with “ipsum lorem” text.