I've been having the same problem but very inconsistently. When I go look in device manager, the COM port shows up. However, in the drop down menu of the IDE, there is no option to select either of the Due ports and the IDE reports the error you described. I've found I have to unplug it, let it sit, and then after a while plug it back in and try again. I've also found it to function more reliably on the rear USB ports of my computer than the front USB. Very frustrating when it happens but at least eventually it does come back.