My issue was resolved with the help of technical support.
The configuration wizard was run & a different Website Root Directory was created.
The installation went smoothly & the additional web server was back up & running in a few minutes.
I think the issue was that the configuration wizard didn't run after the initial setup was completed.
This is because when configuration wizard was launched i didn't see the screen asking to Modify or Repair Database, Website or Services. I saw the screen that comes up asking for database information etc. & that only comes up when the application hasn't already been installed.