I just did a preview of creating collections only from the custom column and here are the results:
Those last five collections that don't begin with the ". " have no corresponding entries in the custom column in Calibre. I don't know where they came from.
Also, there are no custom column entries for ". Clarke", ". Castle", ". Koontz", ". Crichton", and ". Alten". Hmmm. I believe those are all related to the five collections that don't begin with the ". ". For some reason, the plug-in is splitting up a collection name like ". Alten, Steve" and creating ".Alten" and "Steve" collections in addition to the existing ". Alten, Steve" collection.
That my theory, anyway.