I'm afraid we cannot help with modded games here at all. Does this also happen in a campaign that's never has any mods used in it, AND was started since 1.9.0.4 came out?
Right click on ck3.exe , properties, compatibility. Tick "disable fullScreen optimisations" untick every other box in that dialog, Apply and exit.
Then in the launcher Game Settings menu, select fullScreen display mode, Vsync off, cap refresh rate at 60.
If it still happens then, please attach here an affected save game file, that's never had any mods used in it - I'll see if it happens here too.