One thing to think about is how much your UserTrack is being transposed on a given style and chord progression. This affects many things and an attack on the same chord played at 80BPM will sound a little different at 140 BPM. The audio gets sped up/down. Any chance the start point on a given section is a little too close to the beat and possibly causing the glitch?
Just a thought.

The opposite is also possible, if the chord is late and slower, it won't have the same strum (attack) sound either.

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