I cannot replicate this here, following the steps you took, as long as by “Choose to show it as Fantom USB” referes to changing the “show as” text field in Cubase and not a registry entry.
For a start, in case you haven’t done so already, make sure that your Fantom driver is up to date. By the way, port name changing upon startup, is not coming from inside of Cubase but rather from the OS, and there have been discussions in the past about this. Check this post for further info: Missing (MIDI?) Ports message - #4 by Psychlist1972