It may very well be as you say.
On one job for example, it cut fine for half the work, then the z axis moved down 5mm and continued to cut a quarter of the work, then it got back up to finish the work at the same level. I was not in the workshop when it did this, but since that, I stay around the cnc for the time of the cut. Not very convenient, but hey, it gets the job done for the time being.
It seems like tis pwm setting creates some noise now and then, as the symptoms of the problem look a lot like electrcial noise. Still, I cannot tie this noise to anything. Seems random at the moment.

I don't know what to fix or change yet, so I'll continue to cut and take notes of future strange events, maybe I can pinpoint the cause. I'll update the post when anything new comes up.

The strange sound, to my best ability to explain, is like the motor reduces the speed (low tone) for just a sec (when it loses 5mm), but there is no speed reduction in the gcode. It seems (but I am not sure at all), that this event occurs when the z axis moves up (to safe z).

Meanwhile, thank you. :)