arinlares:
I'm not quite sure I have understood your report, it's left me a little confused
Anyway, for Midi support Milkytracker uses a 3rd-party library called RTMidi - this has nothing to do with Jack or the audio driver.
For audio, there are 4 drivers for Linux iirc:
Alsa
Jack
RTAudio - a closely related cousin to RTMidi, but it provides cross-platform audio support
SDL
So selecting Jack as the audio driver should make no difference to Milkytracker's Midi functionality, as it is entirely separate.
PROGRAM_IX:
I don't know what name the Jack audio driver has on your distribution, but libjack0 seems a likely candidate (perhaps it's version 0.xx).