I had the same problem this evening with the story steltek reported on,
http://www.tthfanfic.org/Story-30822 , when I tried to update it an hour ago. I downloaded your debug version and still had the problem, but a few minutes ago, after I opened and closed calibre several times, it updated successfully.
I saved debug logs both before and after I installed your test version. Would you like me to post one or both?