paerpo, используйте WSH — мелькать не будет.
Например:
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Код:

Option Explicit
Const HKEY_CLASSES_ROOT = &H80000000
Const HKEY_LOCAL_MACHINE = &H80000002
Dim strValue
With WScript.CreateObject("WbemScripting.SWbemLocator").ConnectServer(".", "root\default").Get("StdRegProv")
If .GetStringValue(HKEY_LOCAL_MACHINE, "SOFTWARE\New_Prog", "Install", strValue) = 0 Then
If .SetStringValue(HKEY_CLASSES_ROOT, "*\shell\proba\command", "", "cmd.exe /c ""start ""New_Prog"" """ & strValue & "Prog.exe"" %1""") = 0 Then
WScript.Echo "[cmd.exe /c ""start ""New_Prog"" """ & strValue & "Prog.exe"" %1""]"
Else
WScript.Echo "Can't find registy path [HKEY_CLASSES_ROOT\*\shell\proba\command]."
End If
Else
WScript.Echo "Can't find registy path [HKEY_LOCAL_MACHINE\SOFTWARE\New_Prog\Install]."
End If
End With
WScript.Quit 0