One option would be to change the tweak ("Set the list of words considered to be "articles" for sort strings") - then you get the series with the article. However, the tweak affects the titles, too ('Stone, The' as the title_sort for 'The Stone' will be highlighted in read instead of green from now on, and "The Stone" will be the title_sort created automatically in the "Edit metadata" dialog.
I don't know whether there is a less 'invasive' solution available. In fact, I'm surprised by this kind of file saving behavior, considering that all series starting with articles a, an, the are sorted alphabetically under A/T, and not under the first letter of the second word.
// EDIT
Haven't seen your second post. I'm glad you've found the way to make Calibre do what you want it to do
