I have some additional information that will hopefully be useful. I'm not sure if this is a bug in the board or a side effect of the design or what but here is how it works:
The IDE gives the error in the subject line for COM port connected on my windows workstation that I am using to develop. It is connected to the Due Programming port. However, it ONLY gives this error when I have the native USB port also connected that happens to be running Linux. I've tested this both with and without an external 12V power supply connected to the barrel jack. I've also tested this with the native port connected to a different port on the same computer as the programming port. This can be reproduced every single time.
Simply disconnecting the native port for a moment while the upload begins and then reconnecting it after it has started works around the problem but I sure am wearing out my USB ports and cables quick that way