This is an update to this topic.  I have spent considerable time on these issues and here is what I have learned.

This some background.  As you may ar may not know there are multiple levels of config files that start at the Machine level.  They include Machine, a master config, and then the web.config on the default web page if there is one.  Botton line is there is no way avoid these 3 levels if they exists and they build on one another.  So except this fact and here is the work around.

What I have encountered is conflicts in the web.configs running under the default Web Page.  The solution is to identify the conflicts and use <Remove> tags to back out the Default Web page options that are causing the conflicts.  Here are some of the entries I had to add to the Web.configs for the Virtual Dirs running under the Default Web Site.

    <pages>
      <namespaces>
        <remove namespace="DotNetNuke.Services.Localization" />
        <remove namespace="DotNetNuke.Entities.Users" />
        <remove namespace="DotNetNuke" />
        <remove namespace="DotNetNuke.Common" />
        <remove namespace="DotNetNuke.Data" />
        <remove namespace="DotNetNuke.Framework" />
        <remove namespace="DotNetNuke.Modules" />
        <remove namespace="DotNetNuke.Security" />
        <remove namespace="DotNetNuke.Services" />
        <remove namespace="DotNetNuke.UI" />
        <remove namespace="DotNetNuke.Entities.Portals" />
        <remove namespace="DotNetNuke.Common.Utilities" />
        <remove namespace="DotNetNuke.Services.Exceptions" />
        <remove namespace="DotNetNuke.Entities.Tabs" />
      </namespaces>
    </pages>

It's a painful process the first time.  Add a new remove tag...test to find the next one...add a remove tag...till it works.

Hope anyone having these problems get this, understands it, and it helps. 

I've just loaded all the new 4.3 stuff and it totally rocks!!! Got my forum working and it is so sweet. Good luck.

Jeff