I am out of ideas. The best thing to do now is to run calibre in debug mode, do whatever it is you do to make the error appear, then post the debug log.
To get a debug log, do
- Start calibre.
- Click on the down arrow next to the Preferences button
- Choose "Restart in debug mode".
- Wait for calibre to restart.
- Connect your Kobo.
- Wait for the connection process to finish.
- Do whatever you do to get the error.
- Close calibre.
- Post the entire log that appears in a dialog.