Which MIDI driver/back-end are you using (raw or seq) ?
EDIT: I guess that's not quite a QjackCtl issue but a JACK-MIDI back-end one. It just happens that MIDI hardware ports are named sequentially (midi_capture_1, 2, ...?). If you, for instance, power off one of the hardware MIDI devices, it might well happen that all remaining ports will get renumbered and fill in sequence, with no holes.
As QjackCtl client/port aliasing assumes that port names are unique literal names. Let's think you renamed "midi_capture_2" to something like "MIDI In 2", then you unplug the supporting hardware device. Uh. it might just happen that what was previously named as "midi_capture_3" now is automatically named as the new "midi_capture_2", aha indeed. See what I mean?
I guess again this is subject for a bug ticket on the JACK-MIDI back-end -- make sure you get it into http://trac.jackaudio.org/ ;)
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