Thanks, noted about the open permissions for apache.
I've tried a couple of sites now using the scp command to copy to the back up server and each site seems to work fine with this process.
When I use the scp command i'm doing it as root both on the master and slave.
When i set up rsync I created 'someuser' as per this guide
So I guess you're right, it's either down to permissions, or rsync not copying all files. How do i determine which?