How does layer visibility affect inclusion on the final pages?
For non-interactive layers SiteGrinder includes them if they are visible in the current page definition (made with layer comps or SiteGrinder Tool's Page Definer) and excludes them if they are hidden.
Interactive layers and layer sets (buttons, rollovers, popups, and menus) generally rely on the visibility of their button triggers rather than on their own visibility. Layers containing links for buttons (the "-link" hint) or for words and phrases within text layers (the "-links" hint) are never visible on the resulting pages. Their visibility is irrelevant.
Popup layers are an exception if the "No Popups" or "Only popups representing other pages" options are selected on any pages. In those cases the popups that are "turned off" for a particular page will ignore their button trigger and obey instead their visibility.