We have managed to re-create the issue ... it is not so much the active window getting minimised, but rather a "loss of focus" ... causing an underlying window to overlay the *active* one.
To demonstrate this behaviour we start an instance of Windows Explorer, and then fire up Adobe Acrobat Professional 8.0 (via Winflector Client 3.5.8.2) ... saving an open document causes Windows Explorer to "cover" the active Acrobat session.
The Winflector Server is running on MS Windows 7 Professional 64-bit system, while the Client is running on MS Windows 7 Professional 32-bit system. This behaviour is not limited to Acrobat and is observed in other applications as well.
A video screen grab of this behaviour can be viewed at <http://www.youtube.com/watch?v=DmQDqMngVq8>