I have 4 master files, the root and three others for three different basic layouts - those three all reference the root.master. When I edit the root document - the "Corporate Site" at the very top of the content tree - I have four editable areas that work normally. This document is the only one that uses the root template that in turn uses the root.master.
In every other document, the master files have content placeholders with CMSEditableRegions in LiveSite view mode, so they're always visible, but only editable from that root document. Since switching to the CMSPortalManager in my root.master, these sections no longer appear anywhere else.
Here's one example where they no longer display at all either on the live site, or when editing any pages using a template that uses this master file. All the CMSEditableRegions are the ones that have disappeared everywhere except when editing that root "Corporate Site" page.
<%@ Master Language="C#" MasterPageFile="~/Aaaai/Layouts/Root.master" AutoEventWireup="true" CodeFile="Home.master.cs" Inherits="Aaaai_Layouts_Home" %>
<%@ MasterType VirtualPath="~/Aaaai/Layouts/Root.master" %>
<asp:Content ID="HeadContent" ContentPlaceHolderID="HeadContentPlaceHolder" Runat="Server">
<link rel="stylesheet" href="~/Aaaai/Styles/Layouts/Home.css" type="text/css" />
</asp:Content>
<asp:Content ID="UtilityNavContent" ContentPlaceHolderID="UtilityNavContentPlaceHolder" runat="server">
<cms:CMSEditableRegion ID="UtilityNav" runat="server" InheritContent="true" ViewMode="LiveSite" />
</asp:Content>
<asp:Content ID="HeaderQuickLinksContent" ContentPlaceHolderID="HeaderQuickLinksContentPlaceHolder" runat="server">
<cms:CMSEditableRegion ID="HeaderQuickLinks" runat="server" InheritContent="true" ViewMode="LiveSite" />
</asp:Content>
<asp:Content ID="MainContent" ContentPlaceHolderID="MainContentPlaceHolder" Runat="Server">
<asp:ContentPlaceHolder id="MainContentPlaceHolder" runat="server" />
</asp:Content>
<asp:Content ID="FooterMainContent" ContentPlaceHolderID="FooterMainContentPlaceHolder" Runat="Server">
<cms:CMSEditableRegion ID="FooterMain" runat="server" InheritContent="true" ViewMode="LiveSite" />
</asp:Content>
<asp:Content ID="FooterSecondaryContent" ContentPlaceHolderID="FooterSecondaryContentPlaceHolder" Runat="Server">
<cms:CMSEditableRegion ID="FooterSecondary" runat="server" InheritContent="true" ViewMode="LiveSite" />
</asp:Content>