In my C# 2008 application, I use the SerialPort.GetPortNames() function to retrieve the list of currently available ports. What I have noticed is, when ever I plug in a USB
I'm assuming you mean System.IO.Ports.SerialPort.GetPortNames(), because i could not find a GetPortList() function anywhere. MSDN says: "If the registry contains stale or otherwise incorrect data then the GetPortNames method will return incorrect data", so that's probably where the problem lies. I guess Windows doesn't update the registry if the port is still being 'used', just like you can't delete a file when a program has a handle on it.
If you want to test if the device is removed, you can do so with a Window API call (http://www.pinvoke.net/default.aspx/user32/RegisterDeviceNotification.html). Hope that helps!