I was preparing a new update of my Layer Manager tool, and was constantly coming across a lack of quality control in the sub-shape layer assignment in a number of the master shapes in Microsoft provided stencils. I have mentioned this to Microsoft as a bug before but the problem still persists in Visio for the Desktop today.
The layering capability in Visio is pretty comprehensive but can become complicated to manage … without a third-party tool such as Layer Manager. This is because every element in a Visio page can be assigned to zero, one or multiple layers, and this applies to all sub-shapes within a group shape. So, it is possible to assign layers to a group shape without assigning any layers to the sub-shapes. This means that these shapes are always visible and printable, even if you have hidden the layers assigned to the group. This is exactly the issue with a number of the master shapes in Visio, as in the following Home Plan example available from the Sample Diagrams / Maps and Floor Plans category
All layers visible 
All layers invisible
The solution is to fix the layer assignment of the sub-shapes of the master shape. This can be done manually via the Document Stencil, but remember to tick the Match master by name on drop setting. Alternatively, use the new tool in my Layer Manager add-in to correct he master of a selected shape:
This can be repeated for each shape that fails to become invisible when all layers are switch off.
In case I have been unclear, I have recorded a video of this:
Then another video of how the layers can be managed once the masters have been fixed.
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