If you're going to use shelves, just make them through calibre and the driver.
Otherwise what happens when you sync with calibre is that it's definitions of what is shelved where "overwrites" what you have done on the Kobo.
If you add a shelf definition in the driver of just
then all books in a given series will end up on a shelf based on the name of the series.
Probably why you were seeing some books with series info, and some without is that you had added some books on sync #1 with the Kobo, disconnected it, reconnected it and send some more books (in that series) over in sync #2.
When the Kobo was reattached for sync #2, the series info for books that had been transferred in sync #1 would have been updated in the database on the Kobo.