@trebor - if you have chosen to set your library up to be "Last, First" as the default appearance then you should be doing more than just a plain "copy all author sort values to author". You should also make sure that you change your tweak, as per the instruction in this part of the FAQ:
http://manual.calibre-ebook.com/faq.html#id39
Get your tweak right and then try again. Some of my plugins look in that tweak to detect what type of author sort approach users are applying, I can't remember if this one does or not but you should do it anyway. Otherwise when you add new books to the library they will have their author sort all screwed up.
Other than that I confess to not quite understanding exactly what your issue and setup is. If you can include some screenshots showing a specific example in both databases that may help.