The skin editor is where you create all the buttons you may want across all the outputs you create. Some users will create variants of the webhelp.
The webhelp settings are where you select the buttons you want in a particular layout.
What you are seeing is the correct behaviour.
How would breadcrumbs show up unless you either set them in a master page or in the webhelp settings? In the webhelp settings you can define their appearance.
See www.grainge.org for RoboHelp and Authoring tips