[LAU] jack problem

I had this with qsynth, thought it was a problem with this, but then I encountered it with muse. If jack is running, programs will not play MIDI to an alsa MIDI device. If jack is not running, qsynth works surprisingly well and muse (no audio, of course) will play MIDI to a MIDI device just fine. With jack running, trying to manually connect in the qjackctl connections pane will have no effect! Pre-existing connections not involving the jack client program will still work. One possible side effect is that the jack-midi items MAY not appear after this has occured (a few times) and the system will eventually hang. Anyone had this? File bug? Fix or workaround?