On my multiple monitor setup I cannot use full-screen mode, and when I try to use Window mode it always tries to place the screen in the same place which a) does not work and b) isn't where I want it. I have to move the window every time I start the application (which is made very difficult because the window size is larger than the monitor it tries to open the application on) If I capture the mouse, I can't ever move the window at all, which I would like to do.
So, the solution is for the program to remember where I put the window last and always open it there rather than assuming it knows where the window should be. That way I can open the application, go through the gyrations of moving the window where I want it, and then close the application. I can then turn on mouse capture and re-open the application and have it come up on the monitor I want it on at the size I want it with mouse capture. At this point I can't really let my son use the program on this computer at all.