With archive link I mean when you click on Year or Month link I get all yearly or monthly post including post from the excluded category.
The only effect I can see is that the number of post for each month is correct but not when I execute by clicking the archive year/month link.
So the exclude don't work as I thought.
I have tested to change the setting under Extra option to Only expand by clicking the symbol and this works but when clicking on each Month link under each year I get all post again including the excluded category.
So either your plugin don't work as expected or I have a clash somewhere from other plugin that cause this. In meantime when you test the above I will test some more meaning to deactive some category/archive plugins that we have.
I hope the above can help you tp reproduce the issue.