The problems all had to do with polygons on top of each other. The error message that was displayed when trying to define the Boundary Conditions showed the IDs of each polygon.
I have attached the file that I was able to simulate but you will probably need to define the correct boundary conditions in terms of interior and exterior conditions -- I just used the default options, and I'm sure that is not correct. Also, as noted, you need below, you need to properly define the glazing system cavity, probably by importing glazing systems defined in WINDOW. See the document called Quick Start which shows how to import a WINDOW Glazing System into THERM
https://windows.lbl.gov/sites/default/files/software/THERM/Therm7-03-QuickStart.pdf
You can find a specific polygon by ID number using the Edit / Select Special menu item, which allows you to enter the ID. That polygon is then highlighted in the model. In this case, the highlighted polygon had a different ID, and when that polygon was deleted, there was another identical polygon underneath it that had the correct ID.
Here is another example of that problem
Then there were several polygons that were on top of each other, but with different materials -- in this case it was necessary to delete both of the polygons and then fill the remaining "void" with the correct material. In a few cases, the fill void option wouldn't work because the polygon surfaces were not next to another polygon, In that case, the polygon needed to be recreated. I used the "False Die Mold" method shown on page 5-108 of this doc
Here are the main examples of that type of polygon overlap that I found

Once I got all the overlapping polygons deleted, the Boundary Conditions could be generated.
However, another issue with this file is that there is not a glazing system cavity defined for either glazing system. I would suggest modeling those glazing systems in WINDOW, and then importing them into the THERM file, which will automatically create a glazing system cavity based on the properties of the glazing system in WINDOW.
In the example file I have attached, I filled the glazing cavity spaces with a Frame Cavity, just to allow the file to simulate someone properly. But that is definitely NOT the correct way to model the glazing system cavity.
I also had to increase the Quad Tree Mesh parameter from the default value of 6 to 8, in order to get the model to mesh and then simulate.