Yes, you should configure Cloudflare for the domain where Webmin is running to avoid interfering with requests. It’s likely that you’ve enabled advanced security settings and tightened them too much, causing things to break.
Well, I’ve turned off all security (as much as possible ‘essentially off’ setting) and it still gives the disconnect error on reboot. Finally I disabled the Cloudlfare proxy on the host A record and made a rule to remove Cloudflare SSL on the host domain. So, this keeps cloudflare for everything else except Webmin / Virtualmin - which seems to work better.
Just to mention - I was also, occasionally, receiving the pop-up, red windowed, disconnection error message when using the file manager. With Cloudflare disabled this has also stopped.
I’m not blaming you. I’m not blaming anyone. I am very grateful to be able to use Virtualmin instead of Cpanel and am considering paid plans. I was just under the impression that Virtualmin worked the same with Cloudflare enabled as long as you changed the port. Thanks to the good advice here I was able to find a workaround.