Sorry, but, none of those options have anything to do with collection management. Especially the Kobo Utilities plugin.
The collection management is configured in the driver on the tab "Collections, covers & uploads" in the "Collections" section. Look at
https://wiki.mobileread.com/wiki/Kob...nd_Collections for how to change this. And, the most common problem is that the Metadata management option is no longer set to automatic. This is on the "Sending books to devices" page of the preferences.