Hi Sam -
NCrunch does use the .proj file to establish file dependencies for your projects, although this logic is not sophisticated enough to be able to parse the complex and dynamic dependencies that can exist in pre/post build events.
To solve this problem I would recommend you use the 'Additional files to include' configuration option under the project's NCrunch configuration in order to let NCrunch know about your configuration files. Another option is also to ensure all .config files are included as items in the project, for example:
<Project>
...
<ItemGroup>
<None>MyConfigFile.config</None>
</ItemGroup>
...
</Project>
Also make sure that you enable post build events in your NCrunch project configuration. By default, NCrunch will switch these off as very often pre/post build events contain steps that are not relevant to the test environment. For more information about component configuration, there's page in the wiki -
https://www.ncrunch.net/...-configuration_overview
Note that NCrunch will only ever use the default $(Configuration) that is specified in your .proj file - it doesn't follow the build configuration selected within Visual Studio. There is an NCrunch configuration option that you can use ('Use Build Configuration') against a project to force it to use a specific build configuration if the default doesn't work for you.
I hope this helps!
Cheers,
Remco