Hi, thanks for posting!
My suspicion is that you are using a test project that has been built with a target platform of AnyCPU, testing against another project (or referenced assembly) with a target platform of x64. This would work in MSTest if you have configured the MSTest runner to use x64.
NCrunch has a project-level configuration setting inside its configuration panel that allows you to tell the test runner which processor architecture it should use when running tests within a project. It's under 'Test Settings->Use CPU Architecture'. If you set this to x64 for each of your test projects that make sue of the PDFNet.dll file, then this should solve the problem.
Alternatively, a cleaner way may be to build your test projects for the x64 platform - as with an x64 dependency in their application domain, they will never actually run under x86. NCrunch will always use the default build configuration when building a project, so if you set the default build platform for the test project(s) to x64, this should also solve the problem and will give a cleaner result.
Cheers,
Remco