Are you sure? Because I am 100% certain that the submod needs to be above the orginal mod. I tested it, while it was below and a lot stuff was missing.
This is not noticable, when you added new files, but when you change existing files from the orginal mod, it means that when the submod is below the orginal mod, the changed file will not be used, but the orginal file will be used.
You are probably right from what I can remember how that was coded. Any idea if it was solved in eu4?