Looking at your problem further I don't think the issue is with the Menu system as the page you provided with the Links is a Category List view which is getting its details from the Category not the Menu.
If you go to Content->Category and look at the list of Categories, next to the name of the Category is the Alias in Brackets and in there is the actual name used in your links. I suspect you will find a lot of them have a '-2' added to them from when you did a 'Save as Copy' or similar function to duplicate the Category.
I would go as far as to say your site is mostly made up of one Article per Category or Menu which is why you are getting confused. There are better ways to manage your content that will make managing your site a lot easier and more friendly to search engines. Essentially one category, say Blog, should have lots of Articles, not a category for each article.