After experimenting a bit more with the 3.0 FW I noticed there has been some changes to how refresh rate work.
I was using TVHZ to change between refresh rates before and now I find it is not usable.
It appears the changes via TVHZ are now changing the HDMI settings (Special settings on SATV) too, before 3.0 selection "Application setting" always reverted back to the original 60hz, but not anymore.
This doesn't seem to be a big deal but there are some other issues:
-If you change the refresh rate when the Netflix app is in certain screens (Pause screen, movie details screen), a weird thing happens that when you try to resume Netflix app, it will auto change refresh rate to the previous setting, you need to make sure you select Exit from Netflix app to make sure this doesn't happen screwing the refresh rates.
-If you change the refresh rate via TVHZ (for example to go back to 60hz to use youtube, gaming, etc), for some reason auto refresh rate stops working in Kodi, only solution is to restart SATV.
So in the end if you use both Netflix and Kodi at proper refresh rates, you need to make sure you always change the setting from the HDMI menu, and also when using Netflix make sure you always change it before opening Netflix and exit properly before changing back to 60hz to make sure it doesn't get screwed when you open Netflix again.
Not sure what was the point of these changes but it certainly was more usable on previous FW.