Let me be *real* stupid here -- we're talking about just the Book Title metadata, right? Not the file name or the sorting title?
If so, I understand just fine. On the Kindle forum it was suggested that they would sort correctly if the pub dates were in there (and, I assume, put all the series books in a single collection if the author wrote more than one series with crossing pub dates) but I'm a little suspicious of that -- it doesn't seem to me that this is the case at all when I use mobi books in Kindle on my iPad (admittedly a very different beast, but one in which there are certain similarities).
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