Peter
I don't know if you have already solved this problem, but I discovered that there is a zero width polygon in your file. No idea how it got there, but if I delete the polygons around the area the program was complaining about you can see it
So that is why THERM was complaining about overlapping polygons.
What I did was basically to copy the individual polygons into a new file and then you can create boundary conditions and simulate the model.
I first set the locator at the upper left of the entire model
Then I selected the top set of polygons
And copied them into a new file
Going back to the original file, select (by hand) the remaining polygons except for the polygon that may have been causing the problem
Copy those selected polygons into the new file. They will be placed in the correct position because the locator is the same in both files (because of how you set it at the beginning).
Draw the final missing polygon
Save the file, generate the boundary conditions, and simulate it.
I have attached the file I created this way that simulates. You will want to change the BCs because I just set them to the standard NFRC exterior and interior records.
Let me know if you have more questions.
Robin