I filed a bug report for this already, but I'll post here in case anyone else has the same issue and wants to chime in.
Here's a project demonstrating the issue:
https://github.com/jasonkcarter/NCrunch-DeploymentItem
Instructions
Pull the repository
Open DeploymentItemProject.sln using Visual Studio 2010, 2012, or 2013
Build the DeploymentItemTest project.
Enable NCrunch and do not ignore any test projects (if it's not already enabled)
Notice that the one test fails
Open the Test->Test Explorer (VS 2012/13) or Test->Windows->Test View (VS 2010) windows.
Run the one test and notice that it passes.
If you have Resharper installed, run the test with its test runner as well, and notice that it passes.
It seems as if NCrunch has a problem with files from referenced projects that are marked in the Properties panel (F4) as Copy to Output Directory equal to either "Copy if newer", or "Copy always". If the file isn't in the test project's .*proj file, NCrunch doesn't see it.
The only workaround I've found that is effective is the following.
Workaround
Right click the Unit Test project in Solution Explorer
Select Add->Existing Item
In the lower right, select All Files (*.*) from the dropdown
Navigate to the DeploymentItem file(s) and select it/them
Expand the dropdown on the Add button and select Add as Link
In Solution Explorer, select the files you just added
Open the properties panel (F4)
Set the Copy to Output Directory option to either "Copy if newer" or "Copy always"
Hi, thanks for posting this issue. I really appreciate you taking the time to submit the sample solution as this always make analysis of such issues much easier.
Although this may be a surprise, this behaviour is actually by design. NCrunch uses a build optimisation that allows it to build projects individually, outside of the normal VS build chain. In order for this to work, NCrunch isn't able to copy dependencies upwards into referencing projects because doing this requires a rebuild of every referencing project, then every project referencing these projects (thus completely invalidating the optimisation).
When experiencing problems with this behaviour, people usually observe it through assembly referencing issues, but it does also apply to files marked to be copied to the build output directory. The documentation is geared more towards helping people identify/resolve assembly referencing issues rather than the one you've reported, which perhaps might need to be revised - http://www.ncrunch.net/documentation/considerations-and-constraints_assembly-colocation-assumptions.
Anyway, to turn off the build optimisation that is causing this problem, just set the Copy referenced assemblies to workspace NCrunch project-level configuration setting on the test project to 'True'.