Once in a while, I also got into a situation where I have this focus problem. And once it happened, I think it stays like that until I restart the process?
As a matter of fact, I am experiencing this right now. When I hit the PAUSE/BREAK key, FARR doesn't come up as the foreground window. It's hidden by my browser window from which I am typing this msg. If I resize my browser, I can see FARR was actually brought up and its editbox has the focus (the caret is flashing). So I am now in a state where I have double flashing caret (one in FARR, one in my browser), and when I type, the characters go to my browser's editbox as opposed to FARR.
I am using the latest farr build (v1.09.04)