If you are dealing with an Azure WebJob - I had to remove the following after upgrading to the latest 4.6.1.
<compilation debug="true" targetFramework="4.6.1">
<assemblies>
<add assembly="System.Runtime, Version=4.0.0.0, Culture=neutral, PublicKeyToken=b03f5f7f11d50a3a"/>
</assemblies>
</compilation>
Hope this helps.