Hi savinoff,
even with your MIDI file and the HALion program is it not possible for me to reproduce the behaviour you described above.
With Cubase 9.0.20 build 209 (64bit) and HALion 6.0.15 build 1041 (64bit) it works as expected here with a RME Babyface Pro.
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What will happen if you select all MIDI notes of the MIDI file and cut down their length in the key-editor step by step while playback?
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Which Audio Interface are you using? Can you try different “Buffer Sizes” with your Audio Interface?
best regards
Gerrit