Adam,
I'm not sure what would be causing your described issue. I am not aware of any such obvious issues with our gbXML production. Would you be able to ZIP and attach your gbXML output from Revit? I could look at that for you and see if I could find anything. It would also be very helpful to see some screen captures of your "simple" 4-wall buildings.
The primary cause that I assumed was happening was segmenting of walls due to adjacency. Most people don't initially expect us to handle it that way.
The best way to visualize the analytical model in these cases is to use the Shading Graphics Style, as you can usually see the boundaries if the Analytical Wall Surfaces.
As for suggested analysis partners, much of that recommendation depends on a number of variables regarding output needs, project workflows, experience, etc, so I wouldn't recommend one solution over an other without more information.
As for large multi-story files and gbXML, yes I have seen a great deal of success with this approach, it just requires that Architects be mindful of the way that they are constructing their buildings.
Hope that Helps,
Kyle B
Revit MEP Product Manager.
Message was edited by: Kyle B [Autodesk]
Kyle Bernhardt
Director
Building Design Strategy
Autodesk, Inc.