A curious problem...
I keep several books on-device, wirelessly transferred from Calibre.
In downloading books from the Cloud connection I would direct that the files would adhere to the sorting settings for CC.
The following images need more details.
I downloaded several books from the cloud.
Sleeping Beauty - Broken Empire [0.50]
All books on-device sorted by Series, ascending order.
The results by series:
Blue: Dresden Files
Yellow: Broken Empire [0.50]
Green: Night Angel [1]
Pink: Gears of War
The books downloaded from the cloud connection (Yellow and Green) are sorted, but appear out of position, in relation to the rest of the library which was not downloaded from the cloud, almost as if being contained in a library, within a library. And after downloading several more books from the cloud, I am seeing that the cloud downloaded books are not respecting the Sort setting at all.
Debug log emailed, though I'm not sure if this will show up in it.