I posted my question over in the Calibre forum.
I do believe the underlying problem is with the Kobo not with Calibre despite the fact that the Borders app is not having any problem synching with the device.
Yesterday one time it happened I found that one of the image files was corrupt and I had to get Windows to scan the kobo and fix the file before I could delete it. This time I copied the whole .kobo\images folder to my desktop, batch renamed all the files from .parsed to .jpg in the hope that I could check the preview to see if one was corrupted, but all of them look fine.
I will try loading some books by drag-and-drop and see what that does.