Hi Martin -
NCrunch works by identifying static references between projects, then linking copies of these projects together at run time to build virtual environments in order to run tests. As such, the nature of what you're doing here (i.e. generating custom application domains through dynamic assembly referencing) is certain to give problems with NCrunch. There are ways you can make elements of this approach work with NCrunch, but this will involve give and take with your design.
The
project atomicity constraints can tell you more about how NCrunch constrains this particular design. Specifically, you may wish to look into
tests that build their own appdomains, as this problem area is similar to yours.
Generally speaking, there needs somewhere to be static references between projects that depend on each other - otherwise NCrunch won't know about the dependencies of a project, and won't be able to build an application domain to test it.
Cheers,
Remco