Okay. I seem to have made some kind of difference in the error. I tracked the error down to the specific lines, and on the tables in question I removed the auto_increment from the structure, saved, then reapplied it. Then I ran $LJHOME/bin/upgrading/update-db.pl -r -p --innodb again, and it worked properly. I don't know if this is going to be a permanent fix or not.