Prusa's P.I.N.D.A. XYZ axes calibration fails with generic message "Consult the manual"
One thing, and the one that eventually solved my problem, is to update the firmware. Firmware update instructions: Upgrading firmware - Prusa3D

The only thing you might get stuck on is selecting the right COM port.


Go to the device manager (run devmgmt.msc)
 
In COM and LPT section, you should see port for your printer by name. Select that port number in the firmware update tool.


In my case, I had to run the calibration twice before it worked. I had no problems since then.