Tracy,
Right-click on the title bar of the command window and unselect the dockable property. The same applies to any dockable window.

HTH
>I wish I could get mine to do that! The command window always on top of every other window (unless I dock it, minimize it, or close it) drives me CRAZY. Also the properties window once opened does the same thing. Maybe someone reading this will give me some ideas when they solve your problem...