I think it's likely that there is a specific test causing this problem. I suggest selectively running the tests in groups until you can work out which test (or tests) are doing this. MSTest supported under NCrunch is emulated rather than integrated, so this won't be an integration problem - it's likely to be something inside the test/production code that is tearing down the process, perhaps as the result of a stack overflow, out of memory exception, Process.Exit, unmanaged issue, etc. If you can identify which test is causing the problem, it may be possible to debug into it and isolate the issue.
Another option could be to run all the tests in NCrunch with a debugger attached, then see if the debugger catches any unusual events.