Thank you very much for your quick, detailed and long response Gr5, it'll surely be of great help not just for me but for other people with the same kind of issues. So thanks on their behalf too 😉
I'll try what you suggested whenever I have some spare time and will let you know if it worked out, though I get totally lost when it comes down to Gcodes and Marlin stuff, but I'll figure it out and try to do what you recommended.:
-lower the absolute max acceleration limit in Marlin.
-lower the jerk a 75% more.
In response to your answer, I'll try to be as specific as possible:
No, I do not print through a USB cable, I always print via mini SD card. And yes, both printers run on Marlin -as far as I'm concerned.
I tried using Cura 3.6 and then I downgraded to Cura 3.5.1, I printed the same design in both versions of Cura and with each version I used 3 different settings per print -just to find out and compare the results. Interestingly enough, the shifted layers always appeared at the same heights, but depending on the version of Cura I would get the shifted layers at different heights. I mean, using Cura 3.6, I would get them at some particular point (regardless the settings) and using Cura 3.5.1 I would get them at a different one, that's why I thought the problem could be the program itself and not a hardware problem, having shifter layers at exactly the same points is quite meaningful I'd say.
Also, printing at 0.1 layer height and 40mm/s I noticed that after shifting 2 layers in a row, then it'll get back to its right position and continue printing, which is even weirder to me. I spent hours right in front of the printer just to get the exact moment in which they happened and I got them; and yes, as you said, there was a resonant vibration each time and they normally took place in the transition between the infill and the perimeter of a new layer (infill speeds were down to 40 and 60mm/s, walls were at 30 and 40mm/s, and jerks were at 15 and 20mm/s).
The point is that even having the jerk down to 15mm/s and printing at 40mm/s in Cura, I was still getting them, but when I used Repetier Host, I tried printing at 60mm/s and jerk up to 20mm/s and the print was absolutely flawless. It's not that I can't print, it's just that I want to know why I can't get the results with Cura that I used to get before.
When I use Repetier Host it lets me choose a slicer, either CuraEngine or Slic3r, I chose CuraEngine and used quite standard settings and as I said, flawless prints using Repetier Host. I even tried printing at 120mm/s, quality was obviously affected but no layer shifts whatsoever. So it's definitely something to do with Cura.
Thanks one more time for your time and suggestions, I will reply once I try them and let you know.😃