MuseScore grabs MIDI interfaces
Even if MIDI is disabled for entering notes into a score, MuseScore keeps hold of an external MIDI port. MuseScore seems to search for MIDI ports on startup and grab them all. The only way to keep hold of a MIDI port for use by other software currently is to plug the MIDI interface in after MuseScore has started.
When MuseScore does not need to use a MIDI port, it should release it so that other programs can use it.