ASP.NET problems with 2013 CU6 install

I recently did a fresh install of Exchange 2013 CU6 for a customer and had major issues trying to access the Exchange Admin Centre (EAC) and Outlook Web App (OWA).

The server was a brand new 2012R2 machine.  The AD forest was brand new and composed entirely of 2012R2 Domain Controllers.  Due to an issue they had they completely deleted the entire environment and recreated it.  All servers were installed from the 2012R2 ISO and all Windows Updates applied.  The following problem occurred in both the original environment and the rebuilt one.

After installation the Application Eventlog was full of event 1310 from source asp.net 4.0.30319.0.  This was logged every few seconds.  EAC/OWA was not accessible and simply returned the "Something Went Wrong :-(" error message.  The event was logged for each of the virtual directories, e.g. OWA/Autodiscover/EWS etc.  Details of the event related to "The file specified could not be found", each referring to a different module that was referenced in the web.config file related to each virtual directory, e.g. AntiXSS.