Private Sub frm1_Load(sender As Object, e As EventArgs) Handles Me.Load
...
    Me.Visible = False
  End Sub

      Case WM_MySysTrayNotify 'уведомления Tray -вместо WM_MOUSEMOVE
        Dim lw_lparam As Integer = LOWORD(m.LParam)
        Select Case lw_lparam
           Case WM_RBUTTONUP 'display popup menu
            'Debug.Print("WM_RBUTTONUP")
            SetForegroundWindow(Me.Handle)
            TrackPopupMenu(Me.menu_App.Handle, TPM_LEFTBUTTON,
             Control.MousePosition.X, Control.MousePosition.Y, 0, Me.Handle)

      Case WM_EXITMENULOOP
        Debug.Print("WM_EXITMENULOOP")

      Case WM_EXITMENULOOP
         SetForegroundWindow(GetDesktopWindow())) 

      Case WM_EXITMENULOOP
        LockSetForegroundWindow(LSFW_UNLOCK))
        SetForegroundWindow(GetDesktopWindow())

Public Class Form1

  Private Sub Button1_Click(sender As Object, e As EventArgs) Handles Button1.Click
    Dim Form2 As New frm2
    Form2.Show(Me)
  End Sub
End Class

Public Class frm2

  Private Sub frm2_Load(sender As Object, e As EventArgs) Handles Me.Load
    'В конструкторе: ShowInTaskBar=False, WindowState=Minimized 
    Me.Visible = False
    SetForegroundWindow(Me.Handle)
  End Sub
End Class

  Public Const WM_QUERYOPEN = &H13

  Protected Overrides Sub WndProc(ByRef m As System.Windows.Forms.Message)
    'Debug.WriteLine(m.ToString())

    Select Case m.Msg
...
      Case WM_QUERYOPEN
        Debug.WriteLine("WM_QUERYOPEN")
        m.Result = New IntPtr(0) 'the window about to restore, should return FALSE to prevent from being opened
        Exit Sub
    End Select


    ' Forward message to base WndProc.
    MyBase.WndProc(m)
  End Sub