
Let's check the structure, to be sure:
In your mod folder, there is
- an .ini file, with the same name like the folder
- an Assets folder
In the Assets folder, there is
- a folder called Art
- a folder named modules
Else you have Art\structures\cities\mod_eu.nif (+ other stuff in the folder), and in the modules folder there's the papal states folder (any subfolders within the "modules" folder don't matter, so if you have another folder in between, then this is not the problem).
And in the .ini file, you've changed the ModularLoading entry to 1, yes?
Might be necessary to recheck that, might have been reseted due to some unknown glitch.