When the Newton Backup Utility starts up, it searches for available ports. If a port is in use it does not give the option to select that port. Using a Windows computer configured with a COM1 serial mouse, Newton Backup Utility only gave us the option to connect to COM2 and not COM1. We then installed on another Windows computer that was not using COM1 for the mouse, and Newton Backup Utility allowed us to select either the COM1 or COM2 port.
Newton only lets you select "available" ports. You will see the same results using Windows 95, Windows 3.11, or Windows for Workgroups.