Ok people, here’s how I worked around it.
- disabled ntp: /etc/init.d/ntp stop
- created http://linux.brong.fastmail.fm/2012-06-30/fixtime.pl (code stolen from Marco, see blog posts in comments)
- ran fixtime.pl without an argument to see that there was a leap second set
- ran fixtime.pl with an argument to remove the leap second