Problem with Calibrate Z and Calibrate XYZ Options
I just finished building the printer a couple of days ago and am having the same issue others are having when I run the Z-axis and XYZ-axis calibration routines. I follow the steps and move the Z axis assembly all the way up until it contacts the top end stop. The calibration starts and the extruder nozzle and pinda probe start down to the first point. However, the extruder assembly does not stop at the heat bed but slams into it bending it down.
At this point, I turn off the power to keep from doing any more damage to the heat bed. I have realigned the pinda probe and the bed multiple times but it has not corrected the problem.
The printer Selftest, Mesh Bed Leveling, and Auto home calibration routines work fine. Also, printing from either the included example files or files of my own print fine.
Is there a troubleshooting guide to solve this problem? Also, what information (pictures, videos, etc.) would be helpful to you to assist me in fixing this problem.
Re: Problem with Calibrate Z and Calibrate XYZ Options
hmmm.... sounds for me as your printer "thinks" that there is more z-space between top of the printer and the heatbed.
so the printer moves down the extruder for 210mm but hit's the heatbed a few mm before.
there are two significant points to check now:
1. make sure that the 8mm rods for the y-axis are snapped in correctly at the corner parts of the i3 mk2(s).
2. then make sure that the threaded 10mm rods sit completely down into the notches of the Z-frame.
guess it's #2 at your site 
.
dem inscheniör is' nix zu schwör...
Re: Problem with Calibrate Z and Calibrate XYZ Options
And the correct answer is ...... #3. My wife was reading the forum and found "My Nozzle and Z-Axis want to kill my heatbed" and that turned out to be the problem. The nozzle was way too low because we installed the extruder only to the first detent in the extruder cover. And when it tried to go down 210 mm the nozzle contacted the bed and kept going.
Three things should have led us to this solution: 1) when we were building the printer and setting the pinda probe height I had to push the probe far down in the hole to get it to line up properly which I thought was odd, 2) we had problems when loading the filament where it took like three tries to get it loaded, and 3) the distance from the bed to the top always was under 200 mm when it should have been close to 210 mm.
Re: Problem with Calibrate Z and Calibrate XYZ Options
yeah, sometimes we have to learn from the other gender: they tend to read things like manuals and threads carefully before they start to use/operate an item.
but at all, due to the wrong assembled extruder, the whole z-space was diminished (as assumed before).
dem inscheniör is' nix zu schwör...
Re: Problem with Calibrate Z and Calibrate XYZ Options
Turns out there is a #2.5. Thanks so much for your post Jeff as you led me to a solution!
I'd installed the top z brackets upside down and mirrored. They fit and worked, but had the nasty side-effect of confusing the heck out of the calibration as it reduced my effective z by about 10mm. Sigh.
Wish I'd figured this out before putting two large bumps and a gouge in my PEI.