Disappearing mods

I started a game with the following mods: Kranjzen's Great People, Krajzen's Buffs, Smart AI and JFD's Empire of Germany, but as I closed and loaded the game, the mods were disappearing in the required mods for the save when you click mods in the options window.

What might this be? I already have a bit of this when I used Revolutions in G&K. The mod faded by parts as I closed and loaded the game.

Are you loading the game through the Mod menu? That seems to work for me.