When I use fraps, it only records the window that was active when I press the "record button". So after the boss fights, when I flip to new windows and loot bosses on all my chars, all you see is the mouse moving around on my "main" window. So I guess this is the desired behavior for you - if you have all 5 of your windows viewable on screen at once, fraps will only record the window you currently have selected when you hit your record button.