Interesting. It just went through, but now I have the same problem that I did in anthologies. The download happens, and I get the popup saying 1 good update and however many bad, click ok, but the next step of updating the book does not happen. I'm going to go upstairs and test it on windows to get the URL of the story that's not updating in case that's relevant.
This was not happening this morning under the release versions of calibre and FFF.
Edit: the story is
http://archiveofourown.org/works/6149728. It will not update if I do a group update of all my stories on mac unless I'm in debug mode. It does on windows. I can update it individually and that works.
The good news is I'm no longer getting stuck at 30%, so there is that.