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I can see/ear now the problem, or so I believe. Thanks for taking the time and patience.

It all seems related to the very short time of your MIDI loops.

Truth is, Qtractor (and Qranger for that matter, being exactly the same engine), doesn't play well with MIDI loops that are shorter than 1-2 seconds in length (absolute time). In fact, it behaves awfully and unpredictably bad. To make things worst, upon that nightmare scenario, the audio/MIDI drift correction often gets in between and starts nagging you, alternating faster and slower MIDI rendering. Not pretty and not what you expect, I'm sure. But is what you're experiencing.

OK, you don't have to know the details, but I would recommend you to make your MIDI loops longer, at least longer than 1-2 seconds, that is suggesting you to replicate and span it over two or three bars.

Please try && tell whether that's reasonable.

Cheers