With NCrunch 2.4.0.2, I get an assert failure on one project which used to work just fine, though I cannot say if it started failing after upgrading to 2.4.0.2 (from one of the pre-release 2.x versions), or upgrading JustMock from 2013.3.1211.3 to 2013.3.1320.1 (I did both around the same time).
Screencap of the assert failure shown (sorry, it didn't quite fit on my screen):
Using the Compatibility Mode settings, I found that I need to set Pre-load Assembly References to true, after which the tests run successfully. I found this by going through the settings in the order listed on the Compatibility Mode page, and stopped when the tests started working after changing the aforementioned setting. I could then safely switch the other settings back, and tests still work fine.
(Interestingly, though, NCrunch sees double during test execution: while it is running the tests, it thinks there are two times as many tests as there actually are. After completion, the number drops back down to the correct count.)
The solution I'm testing is an ASP.NET MVC 5 + Web API 2 project on VS 2013 using MSTest for tests and the non-free version of JustMock for mocking (though I don't think I'm using any of the features not present in the free version, if I recall correctly).