I have posted a fix, can you download
http://svn.m0n0.ch/wall/branches/freebsd6/phpconf/inc/filter.incand install to /etc/inc on your m0n0wall (use exec.php to upload and then copy to right location).
Then edit an ipv6 rule (don't have to make a change) and hit the apply button. This will make m0n0 re-run the filter creation, which should now correct the problem