How did you setup the dual screens? Somehow the secondary screen may have been established as the primary screen (i.e. any applications will open in this window first) and your primary is treated as the secondary. I would double check your settings (either through Windows Display properties if you use Windows) or through your graphics card manufacturer's settings. I am not sure how the Linux Distros handle dual screens, but I believe it is the same. I would check your display settings and see how the two screens are established in priority.