Hello Gio,
Thanks for bringing this to our attention. I can confirm that I can replicate the behavior using the last 2 updates of Storyline 360 and that the order of the layers appears to be correct in Update 89 and earlier. I've filed this as a bug with our product team so they can investigate these recent changes. As a workaround, please consider republishing your courses using Update 90 if you need the order of the layers to be correct in the Word output.
We appreciate you taking the time to share this behavior, and we'll let you know when we have any updates to share!
