The Quality Check plugin does not do what epubcheck does. I would suggest adding the epubcheck plugin to the calibre ebook-editor or Sigil and use that to verify books. The other possibility is that the KoboTouchExtended driver is having some issues with creating kepubs. I would suggest either using the old 3.7.0 version available from the
jogouen's GitHub repository's releases page. Personally, my workaround since I only use kepub for ebooks that have multiple large images I want to be able to zoom is to use kepubify to do the ePub to kepub conversion.
If you have the KoboUtilities plugin installed, use it to check the device database. There have been multiple complaints about the 4.41.23145 firmware and database corruption.