Same problem here on the Vero2. updated to Kodi 17 yesterday and Calibration is missing, or rather the option to calibrate the screen is missing from the calibration settings. It now just has an option about the number of buffers to use (?).
My workaround for now was to change the zoom property for the user interface so it fits the screen and then when playing a video to change the zoom value on the video options menu and make that a default for all media. Total fudge though.
Th odd thing is in Settings>>Display it says it is “windowed” and is greyed out so can’t be changed to full screen (even thought it appears full screen). I suspect the video calibration option doesn’t appear when display is set to windowed.