Are you guys using any interesting build steps, such as config substitution? I've seen this happen quite often with people that use pre/post build events to manipulate configuration, but then leave these events turned off in the NCrunch configuration.
Another one to check is whether the file is properly included in the project file so that NCrunch knows it exists.
Have you had a look through the troubleshooting sections? (for
tests and
builds). Skimming through this and the related documentation can help to give a detailed description of how the workspacing needs to be considered.
It's always possible to get this working without needing to reference your normal bin directory - which would be impossible to do reliably as the engine can't guarantee the state of the files in this location.