[popcornmix]

@popcornmix Have noticed that changing the GUI refresh rate only works until a reboot.
I have recently (4-5 days?) switched from DESKTOP (1080p60) to 1080p23.98. The setting is saved (verified) and in fact it still works if Kodi is restarted.
After a reboot it's back at DESKTOP. I didn't check if the guisettings.xml still had 23.98, nor I have a debug log - I can get one tomorrow, it should be pretty easy to reproduce though.

I run with 1080p23.98 as my default resolution (as it avoids the HDMI switching for most content). It is remembered for me on reboot.
I did find when I first tried this I left resolution on DESKTOP and changed framerate to 23.98 and that reverted on a reboot.
When I changed to 1920x1080 and 23.98 it seemed to stick.

kodi does something rather confusing with list of resolutions.
DESKTOP is the HDMI mode you launched xbmc in. It will be the preferred HDMI mode (of the TV) unless overridden by config.txt.

If we assume DESKTOP is 1920x1080, then by default kodi adds 1920x1080 to resolution list twice, and depending on which one you choose, the behaviour changes.
If you pick the DESKTOP one, then reboot with a different display that prefers 1280x720, you get the 1280x720.
If you pick the 1920x1080 one, then reboot with a different display that prefers 1280x720, you get the 1920x1080.

That's why I change the name in newclock4 builds to make it clearer what the two modes are.

It's possible that we should be reporting the list of HDMI modes differently. I'd be interested if another kodi platform produces a different list of HDMI modes than the Pi.

I suspect that where kodi saves and loads the guisettings parameters it may be mixing up the DESKTOP and 1920x1080 modes resulting in the swap you are seeing.
Obviously DESKTOP doesn't have an associated framerate (even though you are allowed to choose one), so if that ends up in guisettings, the chosen framerate will be lost.