Looks like there is an issue on the IIS site preventing the config from being read. One of the easiest ways to identify what lines are an issue is to go to the IIS site in question and then view Authentication. If it throws an error, it typically tells you what line is a problem.
Another thing to try is on the problematic server:
$wa = Get-SPWebApplication https://problemUrl
$wa.Unprovision()
$wa.Provision()
This will remove and then re-provision the web application and associated IIS pool (unless that IIS pool is used by other Web Applications, then you'll want to stop/start the Foundation Web service which will de-provision/re-provision all Web Apps/IIS pools on that server).