@FabianChalmers ...
I could be wrong...but I think you are missing a key part of publishing and/or unpublishing an entire/individual module. From your most recent reply, it seems as though you might be using the button at the top of the "Modules" index page that has the options for "Publish all modules and items", "Publish modules only", and "Unpublish all modules and items".

However, what you really want to be doing (after making an "Assignments" module and adding as many assignments to that module as you want) is to click on the icon I've shown here which will give you three separate options: "Publish module and all items", "Publish module only", and "Unpublish module and all items". Notice here that these options are ONLY referring to the module you are currently working with...not all modules in the course.

The difference between the two areas to pick from is the placement of the word all.
I tested the option to "Unpublish module and all items", and it worked as expected. I did have one assignment that remained published...but I that was because I had a submission in that assignment, so the assignment item couldn't be unpublished.
I hope this helps to clarify things and will help to make life a bit easier for you now. Keep us posted...thanks!
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