smiles are disabled on the advanced view (below the first Submit) I used my magic Mod hat and set that for you
You might want to set that (Kobo) popup to 'Do Nothing' for All file types, just to be rid of it
You don't have another reader/Phone plugged in when this happens? Calibre can't deal with 2 detected devices at the same time
Or did you happen to set 'Connect to folder'?
OK
Time to look at the device driver plugin.
Preferences: Plugins: hunt for) Device Interface... : Kobo...