If any VoiceAttack window is always on top, that'd likely be because you have the "Always on Top" option enabled (a toggle for this can be found in the context menu for the title bar, E.G. by right-clicking the VoiceAttack logo in the top-left corner of the main window)
That option can also be changed using the "-alwaysontopon" and "-alwaysontopoff" command line parameters, which do apply to the active instance (E.G. you can launch another instance of VoiceAttack with either parameter, using the "Run an Application" action, to enable or disable the option for the active instance)