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I've been having the same problem with my ALSA MIDI connections for a few months now. It makes no difference whether the devices are internal or external. However, applying your "fix" to my system fixed my problem as well. My Jack-MIDI was set to RAW as well, and setting to seq now allows me to connect my ALSA MIDI devices again.

This is strange, as I have not changed my JACK parameters in at least a year....but I have upgraded my Jack, Qtractor and Qjackctl many times in that time frame. I just never mentioned it before because I thought the problem was unique to my system, having not until now seen anyone else experience it. However, sometimes I could make the ALSA MIDI connections, but they would not last long, and disconnected unexpectedly never to reconnect again. I'll let you know if this "fix" holds up.

cheers,
Lexridge