This is just repeat of the situation that occured in a previous update, as described in this previous hint -- basically, 10.3.9 overwrites the /etc/syslog.conf file, so if you've tweaked it, you'll need to re-do your efforts.
[robg adds: If you've customized your system, there's always a good chance that an Apple upgrade may overwrite your changes. It's a very good idea to make a full backup of your system before running any update, just in case...]
Mac OS X Hints
http://hints.macworld.com/article.php?story=20050416231437691