Adding new servers breaks all existing domains

We have 15 VPS servers running WebMin/VirtualMin, on a mix of Debian8/9 and Ubuntu16.04LTS. Each server hosts about 10 websites.

Recently, when we have gone to add a new website onto any of them, all existing websites hosted on the VPS suddenly resolve to the new site that has been added. So, if we add http://newsite.com then when we got to http://oldsite.com the contents of that old URL are the new website.

We are now completely unable to put new sites live without every other site on the server suddenly resolving to the new one. The only way we’ve found to get the other sites back is to delete the new website completely through the control panel.

A very quick check in /etc/apache/apache.conf shows that it is still set to load everything from sites-enabled, and everything is still in sites-enabled. We’ve not been able to keep things around long enough to investigate as 9 other websites are broken while this is happening.

Has anyone else seen this? The scary thing is this is not isolated to one server, it’s happened on each one we have tried in the last few weeks.

The latest one we’ve tried is an old VPS we’ve had running successfully for a couple of years, and it’s done it again. That server is running:
Webmin version: 1.894
VirtualMin: 6.04

There’s a temporary fix here: https://www.virtualmin.com/node/59694