Kodi occasionally resets settings on reboot

After the Isengard update (and the one after that) Kodi has resetted its settings (for example resets skin to OSMC and screen calibration is lost) few times on reboot.
I grabbed logs after the reset: http://paste.osmc.io/evopacehuj

It is quite annoying combined with the fact that I need to reboot the device every time I want to watch something (ref. OSMC broken after TV being off).

I had similar situation yesterday - after I’ve restarted Vero (which I need to do, because I have Missing sound after some time Vero runs). So I’ve restarted and all settings were reseted to default. I hoped this was only one time issue, but as I can see, not really.

I have exactly the same problem on my Raspberry Pi 2…
Randomly when I turn it on, he lost all of my settings, including skin, language preferences, etc.
I tried the Kodi forums http://forum.kodi.tv/showthread.php?tid=235538&pid=2081953 which indicated me to submit my issue here.
Do you think I have to create a new thread because my bug was on Raspberry Pi, not on Vero?

When you choose reboot or shutdown, how long does it take until the Kodi screen disappears ? Please time it.

Just like GnF said in another thread: