I have being going through this as well. It seems like that the new mod-loader does not work for certain mods, but works for others.

For now, I could isolate that mods editing the projectiles_tables are not properly loaded, even if the mod manager thinks so

There is a very easy way to test it:

The Parrot Gun in FotS does not have any smoke when firing, contrary to the other artillery, due to CA forgetting to add a value in the projectiles_tables

I downloaded the "Parrot gun smoke fix" mode, but it does not work even if ticket in the mod manager.

If I go into RPFM, and set the mod to be a "movie" mod, which makes sure it is loaded automatically, the mod does not appear anymore in the mod manager, but the Parrot Gun finally gets the smoke when firing.

I don't understand why is this, and how many other mod it might affect, but the mod manager update is clearly a blunder by CA

Try this fix:
https://steamhost.cn/steamcommunity_com/sharedfiles/filedetails/?id=2980081898

Just ran follow the instructions, extract the zip into the main folder and run the .bat file.

It worked for me.