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Where are you looking at the way it's sorting?
In the main Calibre window? Because in there, Calibre sorts exactly the way you tell it to. Click on a column heading and it sorts by that column. Pretty standard for column/row-based sorting. If you're seeing weird results here, it's not because Calibre's doing anything wrong. Maybe you didn't put the series id number in brackets, or maybe you used inconsistent spelling in the series name. Or maybe you clicked on Series first, then Title. If you want to sort on Series then Title, click on Title first then Series. A little counterintuitive at first, but it makes perfect sense if you think about it. And once again, this is the standard way software of this type works.
Are you looking in the library folder itself? Don't do this. Because, don't. Poking around in the library folder is like looking under the hood of a car. There may be occasional times when you want to do this, but for day-to-day operation, you sit in the driver's seat and use the interface that was designed for that purpose.
Or are you looking at the sorting of books as you're adding them to your library? Calibre adds new books to the top of the list, which means if you add several books from a series, it adds Book 1 to the top, then Book 2 above that, then Book 3 above that, and so on. They end up in reverse order, but only temporarily. The next time you click on a column header or go into one of the Edit Metadata windows or restart Calibre, they'll be in the right place.
By the way, you might try the View Manager and Reading List plugins, both of which deal with sorting in different ways.
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