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I'm using all default packages from Kubuntu 8.04 so I'm not sure what might be messed up. I'll admit, I'm not a JACK expert, I just know that I never had problems like this until they came up with that JACK MIDI feature (the -X option). Anyway, I started QJackctl and had it start jackd. Then started Qsynth and ran a couple aconnect commands. Here are the results:

midiman@kubuntu:~ $ aconnect -i
client 0: 'System' [type=kernel]
0 'Timer '
1 'Announce '
client 14: 'Midi Through' [type=kernel]
0 'Midi Through Port-0'
client 20: 'UX16' [type=kernel]
0 'UX16 MIDI 1 '
midiman@kubuntu:~ $ aconnect -o
client 14: 'Midi Through' [type=kernel]
0 'Midi Through Port-0'
client 20: 'UX16' [type=kernel]
0 'UX16 MIDI 1 '
client 128: 'FLUID Synth (5374)' [type=user]
0 'Synth input port (5374:0)'

Since "Enable ALSA Sequencer Support" is disabled in QJackctl, I no longer have an ALSA tab in the connections window, and the only place qsynth appears is in the AUDIO tab of the connections window.

If I execute "aconnect 20 128" I get "Connection failed (Resource temporarily unavailable)" which I don't understand because nothing is using it.

If I execute "aconnect 14 128" it establishes a connection, but that's useless to me because I'm not using the "Midi Through" port for anything, nor would I really even know how to use it. I mean, I know what the MIDI Thru port on any MIDI device does, but the "Midi Through" in ALSA sure doesn't seem to relay MIDI messages received on my UX16 MIDI input.

In my sound system settings in KDE, I have the "audio device" set to ALSA and the "MIDI device" set to the UX16 MIDI interface. I know the MIDI interface works because anything I have that is JACK MIDI aware receives MIDI messages from it just fine.