Panels not seen except by admin
Using Jamroom
Cant really remember how the old version of Site Builder worked. Suspect that your right with the presumption that the menu items need to be added to the menu to make them visible.
What pages break for your skin when using the latest version of Site Builder? Suspect the best way to move forward is to build a new skin then move to that rather than trying to identify the issues with the current one and fix them. Might be easier.