Why does everything change when I don't change anything?

[Dietepiet]

I never had your problem, but it might be something like this:

You might have a patch installed that overwrites some of the multiplayer set files. If I remember correctly, patches add an extra .pak file in the Men of War folder which overwrite some files in the other .pak files. When placing the older files from Game.pak in your modding folder, they again overwrite the patch files undoing the patch, the patch will no longer work.

Just an idea, I have no patches installed currently so I can't check this for you.