I am deploying a new website as my main site and it works beautifully.
All of my applications under the root url work as well, except for one. It is a legacy system (c#
Check the Bin folder for the legacy application. It may simply need you to drop in that DLL. The System.Web.Optimization namespace exists as of ASP.NET 4.5 so it may not even be supported. The legacy App might be older than that.
Bin
System.Web.Optimization