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Ok,
I managed to get the model to intersect and divide after an extensive series of trial and error.
I have found in the past that zones within other zones (IE zones that are completely surrounded by another zone) can cause problems and don't really seem to be recognized by OpenStudio. Within the above model was a small stairwell zone which was essentially encapsulated by a larger zone.
When I extended the stairwell zone so that one face was outside of the surrounding zone the intersect/divide tool seemed to work seamlessly.
This may not be the only factor as I tried just about everything else up to this point but it was the first change I made that got Intersect/Divide to work properly.
Some other things that I've learned are important in this instance:
Thanks for everyone who contributed.