Not sure if this is a bug or what, but twice I used server replication and both I had the same httpd.conf corruptions. Full thread here http://virtualmin.com/node/33943#comment-136022--.
In summary, I was missing this line in one part
and this line in another part:
They MAY have been related to a virtual server which was on its own private IP as it has a SSL, but I am not sure.
I fixed it by manually adding on these missing lines, and it works OK.