Virtualmin not recognising features on a virtual server

I had to reformat my server and I used the backup function to backup each of my virtual servers. Once I reinstalled Virtualmin, I restored the virtual servers but now when I run the "Validate Virtual Servers" function, it does not recognise anything from the restored backups, such as individual settings, etc.

For example, when I run that function, it says

Subversion repositories : Missing SVN Location from Apache configuration
DAV Login : Missing DAV alias from Apache configuration

I already have this in the main httpd.conf but it does not see it. However, if I disable/enable the feature, it adds another directive into httpd.conf, exactly the same as the one that is there! It is like it can not see the original config.

Even Apache still had the config for php4 which I don't even have installed on this new build! Is there a way to get Virtualmin to check through the virtual server and apply all the settings it had before, to this new virtual server or something similar.

Many thanks,

Status: 
Closed (fixed)