Hi John,
In VS2010, MSTest would always set the current directory to be equal to the MSTest 'Out' directory. NCrunch was modelled from this behaviour, though most likely not all test runners actually do this.
It looks as though the behaviour in this area has changed with the VS2012 release. I'm observing MSTest 2012 now consistently setting the current directory to be equal to the build output directory (as you've described).
I'll note this down for future revision. Thanks for letting me know about the issue! If this issue is affecting your tests, you may be able to work around it by using the BaseDirectory of the current application domain instead.
Cheers,
Remco