Welcome Back to the Let's Encrypt Community, Aaron 
Your certificate history can be found here:
Having looked over the information you've provided, let me first state that I'm not familiar with Virtualmin. That said, my experience with ACME clients leads me to a few observations:
- Only 3 out of the 5 domain names are mentioned as failing http-01 challenges with webroot authentication
- The same 3 out of 5 domain names are then mentioned as failing dns-01 challenges with manual (dns) authentication
It seems unusual to try to authenticate two different ways for the same domain names. Were the logs you reported from different runs?
You may find these helpful: