Two possibilities that I can think of.
- In the driver configuration (either KoboTouch OR KoboTouchExtended) there is an option Delete Empty Collections. Make sure this option IS selected. Also do ensure that Metadata Management is set to Auto in Preferences | Sending books to to devices.
- Duplicated shelves propogated from the Kobo cloud. Fix via Kobo Utilities / Database / Fix Duplicate Shelves. Do NOT select Purge Duplicate Shelves and DO a sync with Kobo after cleaning them up.