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Hmmm... I assume you're also using one of the JACK-MIDI drivers available, either "raw" or "seq" (see in Setup/Settings/MIDI Driver).

Try restarting jackd with either one, and retry the ALSA connections. It has been to my experience that using the "seq" driver has some nasty interferences as to disappearing or non-effective ALSA MIDI connections. If you actually need to connect external MIDI devices to/from JACK-MIDI, I recommend you to use "raw". If you want to have "seq" as your JACK-MIDI driver, you should abstain from using the ALSA Connections tab and you're better off disabling ALSA-MIDI altogether (ie. turn Setup/Misc/Enable ALSA Sequencer support off).

YMMV.