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You have hit one of the "funky" things in Calibre, where it allows you to specify an author sort at the "author level" as well as override it at the "book level". If you choose Manage Authors from the Tag Browser pane, it will show you what the default sort is for all your authors (this would have come from when you first added a book). Go to those authors that you have a problem with and you will see in there that your "default" is incorrectly set to the uppercase versions etc.
As soon as you fix that, it means in future your author sort will be set correctly for any books added for that author to that value.
There is a long reason why that you can find elsewhere in these forums and possibly on the help page for author sort as well - but Quality Check is doing the "right thing" by telling you of that inconsistency in your database.
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