I've seen a similar behavior on my XP system. It will allow parts of windows to be drawn outside of the viewable desktop area on a CRT monitor. While we are waiting to hear of a complete solution, here are some "stupid keyboard tricks" that I've learned to deal with this.
* With the application selected, press Alt+Spacebar on the keyboard, then press the "X" key. This will maximize the window making it fill the whole desktop but no more.
* If you have a Windows key on the keyboard, press Win+D to minimize all windows to the taskbar down at the bottom. Then right-click on the minimized application that you are interested in and select "Maximize" from the little window that pops up.
* If there is no Windows key, press Alt+Spacebar then the "N" key to minimize a window.
* Also, you can grab a window that is off screen by pressing Alt+Spacebar, then the "M" key. This puts the mouse cursor on the title bar of the window even if you can't see it. Without moving the mouse, left-click and hold, then move the mouse and the window will come with it. Once it's on screen, you can place it and size it to your liking.
Finally, when you exit an application, Windows should remember where it was and open it the same way the next time.