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First of all, that sounds like a really cool project Matt! I hope you may decide to make this available, I know many people would be interested in a SketchUp alternative.
I would suggest setting up an OpenStudio FileSinkLogger (Ruby example) so you can see any log messages that might come out when you run your code.
You are using the right methods in my opinion; you've probably already found these but here are links to the implementation of these methods in OpenStudio:
Are you drawing interior windows in both spaces in FreeCAD or just one? I don't think that an intersection will create a new SubSurface in one space to match an existing SubSurface in the other space.
If you continue having problems, I suggest saving your model pre-intersect/matching then attach it to an issue on https://github.com/NREL/OpenStudio/issues and tag https://github.com/ggartside who has been working on fixing some geometry issues.