I think you may be out of luck.

From MS technet article http://www.microsoft.com/technet/scriptcenter/guide/sas_wsh_pkoy.mspx?mfr=true (my emphasis)
 Quote:
You might want to run the application in a specified window type, such as a minimized window. Exec offers no control over window style


I can think of a couple of options if it really is a problem for you.
  1. Use WSHShell.RUN instead which has control over the window style. You will need to redirect output to a file and read it in so it's not a great solution.
  2. While you are waiting for the command to complete grab the window and minimise / hide it. The console will flash on the screen.
  3. Start the script from kix32.exe rather than wkix32.exe. If you do this the script will create a console that you can manage, and the WSH Exec will use the same console so you won't have additional ones popping up whenever you run a command. You can SetConsole("HIDE") when your script starts, so it should only be a minor irritation.