Add this to the checklist.
- Make sure that the machine.config you check is from the same Dot Net framework as the application pool your application is running under.
In my case the default application pools was changed from Dot Net 2.0 to Dot Net 4.0. This changed the root machine.config to the 4.0 version. This version contains the “scriptResourceHandler” section as well as others. Thus the duplicate section warning.