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What's the MIDI driver you're telling jackd to use (ie. the -X command line option) ?

If it's -X raw then that explains it: all external MIDI ports most probably will get owned and locked to JACK-MIDI backend and there's no way you can handle connections on those from the ALSA-MIDI side of things, not even from QjackCtl ALSA tab for that matter.

I'll suggest you to get rid of the -X raw JACK-MIDI setup, and bring either -X seq or better yet all around a2jmidid into the scene .

Cheers