In the btnRun_click add this line:

Code:
btnRun.Enabled = False
In order to correctly catch the Exited event Set EnableRaisingEvents back to true

Code:
Private Sub CMD_Exited(ByVal sender As Object, ByVal e As EventArgs)
        btnRun.Enabled = True ' < --- Add THis
        'Me.Close() <- This is what caused the form to close. If you leave this commented the form won't close
        txtConsoleOut.AppendText(Text & "All done!!!")
        txtConsoleOut.ScrollToCaret()
End Sub