Webmin creates virtual host configuration files based on the name of the virtual host. This can lead to problems since the load order of the virtual host directory seems to be based on alphabetical sorting, thus, the host "beta.test.com" might be loaded before the host "default" and become the default host. The Apache convention appears to be to prefix the the virtual host configuration with three digits (e.g. 000-default.conf, 001-beta.test.com.conf etc.) to force the correct loading order.
I'd like to see an option to either change the names of the configuration files that Webmin creates for virtual hosts, or have Webmin provide ordering of hosts and have it automatically manipulate file names appropriately.