Hi Tim,
From what you've described, this is primarily not an impact detection issue. That isn't to say you aren't also suffering from an impact detection issue, but I don't think this is where we should be focusing if re-running the test does not produce an expected result.
It's concerning that attempting to show the workspace gives you no result. Are you using distributed processing at all? If not, this would be a hard clue that something is not right.
Are assemblies built from any of your projects GAC-registered on your machine? This can result in erroneous runtime resolution issues that can manifest as test results being out of sync.
Does the engine give you any warnings at all? Make sure you click the 'Show all warnings' button on the Tests Window to make sure you don't have any important ones hidden.
Finally, the next time the engine gets out of sync, would you mind submitting a bug report through the NCrunch menu? If something is seriously wrong, the logs may give me some clues.