Hi,
I've copied our default website with the exact same settings to a second website within the same installation.
Only a set of default settings are not properly propagated to the frontend, when I currently (for example) change the navigation background color, or the heading sizes, only the default values are used and not the values I've set in "Manage website" -> "Layout" settings.
The only settings that are working is the "Header->General ->Top Layout" setting..
Also when inspecting the headings on the front-end, no extra markup is being added which are set in the layout settings.. For example see attached screencaps.