Generated *.dll.config not copied over when running MSTest

In some projects I have an app.config which when compiled gets turned into *.dll.config in the usual way. What I am finding is that sometimes in TeamCity the *.dll.config file is not copied over.
To get around it I have to explicitly create a file with the same name. Which leaves me with both an app.config and a *.dll.config

From  what I could find out it may be related to process isolation

Any ideas, how to handle this ?

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