The folders containing the books should indeed go into one folder. I have several examples of this. Series has no effect.
I suggest that you check that the spellings of the author are exactly the same: no extra spaces within the name, no periods in one but not the other, etc. If you do have only two books, one way to be sure that the names are the same using the GUI is to set one of them to XXXXX, save it, then set it back to what you want accepting the auto-complete proposition. Alternatively, copy the name from one of the books into the clipboard, select all the titles, and use the bulk metadata editor to set all of them to the copied name. Etc
(edit: itimpi, another case of simultaneous responses.
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