As an additional data point indicating that Magnuss's problem may relate to his specific setup, after installing 9.12 I did a batch polish of six books at once that flew through with no errors.
That said, my experience in the past has been that the "upgrade internals" option, which is checked on the first of the screenshots, is most likely to be related to any later errors. That's far less because of Calibre than some of the idiosyncratic coding and workarounds often found in epubs (example: books that use
instead of
for every paragraph) that makes it difficult to properly update from epub2 to epub3.
Thus, the first step I'd take to debug this is to
uncheck "upgrade internals," close everything, restart everything, and try again.