The display calibration "issue" you are seeing is from fractional and integer frame rates switching to the correct refresh rate (so 60.0hz and 59.97hz function correctly now for example). Up until very recently, this wasn't working correctly (ty kszaq!).However each refresh rate has separate calibration profiles, so calibration must be done for each potential refresh rate. I'm not sure if in the GUI you have the ability to switch between 59.97hz and 60hz for instance, so if not there is a bug there. If so, I wouldn't consider this a bug.
I recommend you leave adjust display refresh rate enabled, and calibrate for each refresh rate in display settings. If you can't select between 59.97 and 60 for instance, you can play one of the fractional 59.97 clips that is "resetting" as you put it, and then while playing hit the back button and calibrate in settings. Do this each time your calibration "resets," and eventually you should have saved calibration for each mode.
I'm sorry I don't have a box in front of me to check the options, but this should work for you.
I don't have the image loaded up on my Nexbox at the moment, but what happened to me was that I calibrated my screen at 1080p 60hz and then exited back to the menu. After that I chose REBOOT from the Kodi menu. When it came back up, the screen was all messed up again, having lost the calibrating I did moments before. I did this twice and both times it did not save the calibration. I never played any video, so the screen should have stayed at the same refresh rate after each reboot and use the calibration settings that I had done originally.
When I have a chance tomorrow I will put the image back in my box and play around a little more with it.
Chuck