On the topic of the Com Port not disconnecting, this is from the ViewPort (Ver. 4.8.2) Help:
Only one Program on your PC can use the COM/USB port that connects the PC to the Propeller chip. Typically you’ll want to use the Propeller Tool to develop new programs and use ViewPort to debug them. Auto-Connect/Disconnect makes this easy by stopping the connection when the ViewPort Window is no longer active (like when you select the Propeller Tool window). The connection will restart when the window becomes active again (when you click on the ViewPort window). You can disable this behavior under “Edit/Preferences”.