The author column is *always* sorted using the author_sort value. If you are seeing it sorted by FN LN, then the author_sort values are FN LN and not LN, FN as you say.
You can fix author_sort values. The first thing to do is go to the manage authors dialog (there are several ways to get there) and check that the author sort value for each author is correct. From reading your posts, you want that value to be LN, FN for author names that are FN LN.
If you haven't messed with the author_sort tweak, then the button 'recalculate all author_sort values' should produce close to the right answer. Press the button and *look at the results*. If you like what you see, then press OK and the author_sort values for the books will be changed.
If the values for authors are correct, then you must force recalculation of author_sort for each book. Select every book that is wrong (perhaps select the entire library), press the 'E' key to get to Edit Metadata (bulk), check the "Automatically set author sort", and press OK. The author_sort value for each book will be recalculated using the sort value for each author that you see in the manage authors dialog.
If you haven't done so already, you should read the calibre manual section on author management
http://manual.calibre-ebook.com/faq.html#id34