I do know that I once tried to get a free "throw-away" certificate from a commercial SSL vendor for an internal test server for a university project (the faculty members evaluating the project would have freaked out at any warning or approval request message). The vendor would not issue the certificate because of the .edu main domain being registered with another vendor....
This one “is generally the result of a buggy client” requesting permission to obtain certificates but then not actually obtaining them. Do you have a system administrator responsible for your Virtualmin Pro installation? Is it shared with a lot of other users?
Seems like we might be having the same problem as the University of Alabama and RPI? We’re actually the only group on campus using LE that I know of, so I don’t think it’s a problem where all the other IT groups with their respective domains are impinging upon the rate limit. Is there anything that can be done?