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It seems to happen on one machine only, a 10 year old Sandy Bridge Core i5. More and more I don't think it's a Qtractor bug but a timer glitch on the machine.

AFAIK the system timer is on most systems tsc but it can be set to hpet. And there is snd_hrtimer.

Is it possible that Qtractor uses different timers for audio and MIDI and how can I ensure that the same timer is always used? By setting the MIDI queue timer to "(default)"?