Thank you for sharing the model, @merkurettra! I can recreate the issue. Something strange is going on in this model that I haven’t been unable to pinpoint. I will document this for @ksobon to have a closer look.
I will let you know once we have a new release with a fix. Meanwhile, you can use the Import Windows functionality to add the windows to the rooms from inside the Model Editor.
Here is a recording that shows the process.
Let me know if you have any questions.