[DNSB]

The Kobo reader device interface shouldn't be an issue whether it is enabled or disabled so I wouldn't worry about that driver since it is only for the original and Kobo WiFi readers. Having both the KoboTouch and KoboTouchExtended drivers enabled can cause issues. In the Plugins section of calibre's preferences, I would search for KoboTouch. At this point in time due to issues with the KoboTouchExtended driver when converting to kepub on the fly, I would recommend using the KoboTouch driver. So if the KoboTouchExtended is not greyed out, click on it and then enable/disable plugin. If the KoboTouch is greyed out, then select it and click on enable/disable plugin. You can also do this from the KoboUtilities Driver menu item.

On the second page of the KoboTouch/KoboTouchExtended driver configuration, check and make sure that Do not treat replacements as new books is unchecked.

Then I would suggest manually removing the books sent to your Kobo and then power cycling it.

After the power cycle, pick one book in calibre and open it with calibre's editor and run bugcheck on it (icon on the editor's toolbar that looks like a bug with an ! on it's back). If there are any errors, you can try fix automatically. If that looks happy, then open the book in calibre's viewer just to make sure that it is viewable. After that, send the book to your Kobo. Check that it is in the correct directory and the filename ends in .epub from Windows Explorer. Safely eject your Kobo and see if the importing screen (black screen with a bar starting at 6%) comes up.