There's a lot happening here that I'm not sure if I completely understand, though I suspect this is related to the default configuration specified in the project file.
NCrunch will always rely on the default build configuration and platform that is specified in the project file when running its builds. It does not consider the chosen target platform within Visual Studio itself, and as such its builds far more closely resemble a command-line invocation of MSBuild.exe against the project file. If you see this again, make sure that you've specified a default platform inside the .proj file's build XML that makes sense given your development context.
Metro apps aren't yet officially supported by NCrunch. Hopefully this will be introduced later down the line as the WinRT platform matures and more documentation becomes available. NCrunch may work well for you on your project, or it may be a bit hit and miss..
Cheers,
Remco