I've had a lot of trouble upgrading a couple of computers from 8.1 to 9.3 on Windows 7, especially when there are two Digi Neo 8 devices present.
Usually the first card upgrades fine (the Ports actually are still using the 8.1 driver, though) and when I upgrade the second card, I get a blue screen. On reboot the two cards are using different driver versions (the first upgraded card has 9.3 and the second has 8.1). Upgrading the second card, it will complete, but now the COM ports are numbered much higher than desired.
Now that I understand these high-numbered COM ports are related to the phantom COM port issue, I can correct it using the Digi Knowledge Base article. This has been successful in every case.
Typically I will then need to right-click and 'Upgrade' each COM port in Device Manager as the ports do not pick up the updated driver version.