I have a custom Series column that I can populate manually and it works just like the default Series column.  However -- I can't update the custom series column for a group of books by using the Edit Metadata dialogue.
The custom column appears in the dialogue, and I enter the series name, check the box to auto number books, and check the box to force the start number. When I apply, no information appears in the library column.  Nothing.
In fact, if I select a group that already includes manual series entries, and follow the same process, the manual entries disappear.  All blank.
The default Series column works perfectly, as always.
I don't know if I'm missing something, or there is a problem in calibre.  I did not try this while on 5.x, so I don't know if this has something to do with the 6.0 update.  I'm stumped.