It's not necessarily a bug so I'm raising it here rather than github.
When you click inside the window when it does not have focus, the game doesn't respond to that. For instance, if you try to select an element, nothing will happen. If you try to draw, nothing will happen.
Do you think this is desirable or not? Personally I think it's bad because the window still responds to mouse movement, e.g. an element will receive a red outline on hover and the pen will move around.
Dammit, once again I forgot to test in "normal" TPT. It was your mod this happened in.
Yes, the latest release responds properly.