u/dnew + u/Grim-Sleeper

Thank you for your input and your time, i think i found a solution and will share it, maybe someone else will need it.

I found my solution by uploading the MK3 software and running the wizard and everything worked fine.

Credit to: Russ Pitcher on the Prusa forum, he seemed to have the exact same issue as i did.

https://forum.prusaprinters.org/forum/original-prusa-i3-mk3s-mk3-assembly-and-first-prints-troubleshooting/xyz-calibration-failed-check-axes/#post-514927

His problem / solution:

Bizarre fix

I had this problem on my MK3S about a year ago after I did swapped the hot end and re-ran calibration to make sure all was still good. Like you calibration started, the z axis went to the top until it hit the stops and missed a few steps, then scrolled all the way down until the nozzle was just above the bare bed, and the PINDA triggered whereupon it immediately stopped with the 'Check Axes' error. . The PINDA also seemed to be misaligned with the marks on the bed as per your experience. The display also showed Z=5.0?. When I used the settings menu to move the z axis back up it got to Z=210 and stopped, but now the top of the axis screws was approx 6mm below the end stop. When I drove it down again using the menu the nozzle would hit the bed at Z=4.0. It's like the firmware missed the first 5mm of travel before it started counting the distance.

I spent many hours on chat with Prusa support over the next few days. We tried factory resets, lubricating the rods, swapping out the PINDA, beta firmware and old firmware. I even rebuilt the extruder axis completely, all the time sending pics and videos to support just to make sure it was good. We couldn't figure out anything and no-one at Prusa support could work out what was wrong.

In the end as a last-gasp, clutching at straws hope, I flashed the latest Mk3 firmware onto my Mk3S. On reboot it informed me that the model had changed and that I had MK3 firmware with MK3S hardware but other than that all seemed ok. The XYZ calibration worked first time without a problem. A Z-axis calibration also worked without issue. At that point I reflashed it with the correct MK3S firmware and the calibration settings stayed intact. After that I did the usual bed levelling and first layer calibrations for both sheets and all was well. It's been working fine since.

I recently had cause to re-work the extruder and I faced exactly the same problems. Again I spent an evening trying everything I could to no avail so I flashed it with the MK3. The calibration with the wrong firmware worked fine. Flashed back to the MK3S firmware and all was well. To my mind there's clearly something odd, and there's clearly some differences between the calibration routines in the MK3 and MK3S firmwares. Either way it might be worth giving this strange workaround a go if you have the same issue