>I am sure this is related to the update of Windows 7 because I didn't had that behavior before. Basically, when I compile a project, despite the fact that I have the bottom window to be the Error window, the Output window will appear on top of it. I close it, recompile and it keep showing up. I never had that behavior under XP Pro. Does anyone know how to avoid that behavior?

Unlikely to be Win7 related.
Make sure that Tools/Options/Projects and Solutions/General : "Show Output window when build starts" isn't checked.