Hi Phil -
NCrunch will always use the default build $(Configuration) and $(Platform) that is specified in your .proj files. This can sometimes be a cause of confusion for people, as the build configuration in the Visual Studio IDE allows you to choose (and thus inject) different values into the build for these two properties. Basically this means that if the build settings in your project files are out of alignment if your IDE, then you may experience different build behaviour to what you are expecting.
The logical solution to this would seem to be for NCrunch to try and follow the selected build configuration within Visual Studio, although there are huge problems with this approach. The chosen build configuration can have implications for the logic and structure of the source code under test, and as such every change to the VS build configuration would need to be associated with completely throwing away all code coverage information and test results. For solutions with tests that can run through under 30 seconds this isn't a big deal, but NCrunch is often also used with solutions with test running times into the hours, for which throwing away this information would be particularly painful.
NCrunch does contain a project-level configuration setting, 'Use build configuration', allowing you to specify which value should be injected as the $(Configuration) MSBuild property. My usual advice is to try and align your .proj build defaults with the configuration and platform you would normally use while developing in Visual Studio, as this is generally better practice and can also help you when working with other tools (such as build servers).
Cheers,
Remco