I finally found the solution after much trying.
The key was in the Assembly load trace.
LOG: Redirect found in application configuration file: 1.0.0.0 redirected to 1.1.0.0.
Here are the steps I took to resolve the issue. It might be possible to skip some of these but this worked for me:
It will look something like this:
<assemblyBinding xmlns="urn:schemas-microsoft-com:asm.v1">
<dependentAssembly>
<assemblyIdentity name="System.Web.Optimization" publicKeyToken="31bf3856ad364e35" culture="neutral" />
<bindingRedirect oldVersion="0.0.0.0-1.1.0.0" newVersion="1.1.0.0" />
</dependentAssembly>
</assemblyBinding>
I don't know where this section came from in the web.config but having removed it everything seems to be working once again.