correct on both counts.
Then i am confused by your statement “a sudden influx of phone calls…” from clients?
Are you hosting clients with Webmin in addition to Virtualmin and on the same system?
I am just trying to recall if i even run a letsencrypt ssl on my webserver administrator interface…EDIT oh i have got letsencrypt running for webmin and mine is working fine.
Why are clients complaining exactly and for what service (webhosting or email?)
dovecot and other services use a san on the webmin certificate, due to lack of sni support at the time.
automatic renewal of the webmin certificate worked fine for the first year or so. then one day…
bump
just realized this topic turned two yesterday. now where are my candles…
bump
kinda spooky how long this has been outstanding. 
Please read here both post you see they need time for some more then only LE.
AND LE script is maybe in work at virtualmin.
https://www.virtualmin.com/comment/818437#comment-818437
https://www.virtualmin.com/node/67390
Ofcourse you could still have an other problem as cause
You HAVE GPL TPNsolutions asked you to skype him, and you can open a support ticket at virtualmin ?!?!
my issue predates that.
YUp we all know.
BUT pointing out it makes no sense to solve your issue, and not solving other parts out of links i posted.
Meaning if they are working on new version of script , they will test ofcourse and then probably if your issue is caused by a bug also solved.
Solving a issue in for now outdated script makes no sense!
IF NOT BUG, but something with your situation / config we did post some notes where and how to get help.
Also if you really wanted help to solve it you could get payed support ( also long time ago) to solve your issue, even one Person is offering you to help by skype??? .
Even his emailadres is here above in topic from tpnsolutions
I’m on CENTOS 7x and there no problems! Only with that acmev1<>v2 ofcourse now
bump
Why don’t you read?
The links and follow there for Letsencrypt Virtualmin Work
As they write here >
https://www.virtualmin.com/comment/819452#comment-819452
As simple all is in work an newer script part , and makes again i wriet nosense to solve your problem with old depricated script!
So bumbing makes no sense to, while as i did write to solve your problem sooner only for you you have to pay someone for special support yourself.
new version of webmin, certbot installed, same problem as before. :’(