As a two-monitor user at work, I\'ve noticed that applications behave differently with regards to what monitor they open on (primary or secondary monitor, the last monitor the a
As a windows programmer I control the starting monitor of windows created by my apps by a. storing my apps last position in the registry and restoring that, and b. lacking stored info, setting the starting position to magic flag values that windows uses to position the app using its default logic. The default logic changes from OS to OS as MS improve the user experience, but tend to ensure that the app will open on whatever monitor the user is most likely to be looking at.
As a user with a multi-monitor Windows XP / Vista system I'd use the nVidia desktop manager that has the ability to set starting positions for applications otherwise don't have appropriate behaviour.