Yeah i know that problem. When some annoying text baloon pop's up from the system tray, my game usually slows down. Sometimes, it goes from 400/500 FPS to 100/80 FPS.

It's very weird that your FPS increases when the window is partially covered.
I guess you have enabled V-Sinc (look at the parameters you pass to D3D when you create your device). That causes your app to run at 60 FPS by default.

Are the content's of your screen updated when another screen partially covers the window?? If not, i guess that's the reason why your FPS increases, because Direct3d doesn't update the window.

Maybe you can show me your render loop code?