Hi Nick,
Thanks for sharing this issue, it was a good find.
Apparently MS recently introduced changes to the build targets used to prepare a project prior to its build. These changes included the introduction of a target responsible for assigning a default value to the 'Link' metadata item on EmbeddedResource project items. The change itself isn't compatible with an area of the build NCrunch overrides, so the target isn't being executed. This means that the 'Link' metadata isn't being set automatically for embedded resources inside NCrunch builds, so the namespace isn't being correctly calculated when the resources are being attached to the built assembly.
As you've already discovered, assigning a 'Link' tag to the affected embedded resources will allow you to work around this problem. This is the cleanest way I've found to allow you to continue to function with this issue.
A fix for this will be available in the next version of NCrunch.