Thanks for the response, that page is very helpful. I did some further digging and found that the font is included in the project according to Visual Studio. I also had a look at the project file and found this bit:
<BlendEmbeddedFont Include="Fonts\UniversLTStd-ThinUltraCn.otf">
<IsSystemFont>True</IsSystemFont>
<All>True</All>
<AutoFill>True</AutoFill>
<Uppercase>True</Uppercase>
<Lowercase>True</Lowercase>
<Numbers>True</Numbers>
<Punctuation>True</Punctuation>
</BlendEmbeddedFont>
There are more BlendEmbeddedFont entries in the csproj but this is the first one. As far as I can tell the build process embeds this font into the exe.
I added the extra entry:
<None Include="Fonts\UniversLTStd-ThinUltraCn.otf"/>
This change made for all the embedded fonts in the project meant ncrunch could build correctly. However, it's not going to be possible to ensure that everyone adds those None entries when they use Blend to add fonts to the application, and I'm worried we will get projects suddenly not building, rendering ncrunch useless without anyone on the team knowing how to correct it.