Necro-ing because I believe I found the problem.
I think when a user has DisplayFusion enabled (which I do) and tell it to restrict one of the screens (the unused 4th screen above), it creates some kind of virtual monitor that hides the topography from applications like Input Director. I cannot remember which other application had an error that caused me to investigate DisplayFusion but it had similar "Wait, why is it not behaving the way the physical screens would suggest it should?" issues to Input Director.
DisplayFusion users should not disable screens in Monitor Configuration. This can cause problems for Input Director.