Well, NCrunch seems to be handling the MSBuild stuff just fine.
The issue is that NCrunch isn't keeping the whole solution structure consistent, just the individual projects. I'm sure there is a reason it is done that way, but my particular template relies on cross-compiling, basically.
I have already pushed a bug report, so that you have the build log.
However, for a simplified example, imagine this:
2 projects, ProjectA and ProjectB.
The solution has this structure:
Code:Solution.sln
ProjectA\ProjectA.csproj
ProjectA\File1.txt
ProjectB\ProjectB.csproj
ProjectB\File2.cs
ProjectB has the following post build step (overwriting its File2 with ProjectA's File1):
Code:copy ..\ProjectA\File1.txt File2.cs
The post build step would fail (under NCrunch) because there is no "ProjectA" directory from which to pull.