EDIT: This was previously entitled \"App Init behaviour different between IIS Restart and Application Initialisation\". I have changed the title to expand t
Well the post mentioned in my comment above led me in the right direction and then I found the answer on this post: Difference between AppDomain.GetAssemblies and BuildManager.GetReferencedAssemblies
So my code was changed to var assemblies = BuildManager.GetReferencedAssemblies();