Hi Archie -
Colour configuration for the NCrunch tool windows was a late change in the 1.42 release, so as-yet there isn't any VS integration behind this, although it is possible to change the colours of your tool windows via the NCrunch
configuration panel. To a limited extent, this can allow you to align NCrunch with your VS colour scheme. There will likely be more improvements on this area in future.
Cheers,
Remco