Hey Jamie,
http://www.virtualmin.com/ticket-tracker/bug?bug%5fnumber=34&f%5ffix%5ff...
Sounds like the bootup and shutdown stuff isn't quite right in the latest Webmin.
To to have a service started on boot (for example):
chkconfig --level 345 httpd on
Or not started:
chkconfig --level 345 httpd off
Status:
Closed (fixed)