Either playback via Jack or midi input via Portaudio but not at the same time
As suggested by this comment here, when JACK is used by MuseScore to pipe output to one's soundcard MIDI, there is no option in JACK (using Portaudio) to wire a MIDI keyboard to act as an input device for MuseScore. It shows MIDI Out only. MIDI playback works great, but i'd like to have MIDI input too.
This was tested under Windows 7 on ver 0.9.6.