ServerAdmin wipes changes to apache2/site/* files
If you change the configuration for any site using the Mac OS X Server Admin tool, it will rewrite every single site file in the /etc/apache2/site/ folder. Do not change these by hand if you use this tool.
This is somewhat braindead as for example to use pretty permalinks in Wordpress you need AllowOverride FileInfo for that <Directory>. However the only choice that Server Admin gives you is AllowOverride All.