This problem seems to be related to how the template shares the App.xaml file between projects in the solution.
Visual Studio has slightly different build logic compared to MSBuild when processing a solution as a whole, so I can only assume the difference is allowing it to work artificially. This is probably how the issue managed to progress as far as it did (the RC build).
The problem seems to be caused in line 441 of Microsoft.Windows.UI.Xaml.Common.Targets, where the XAML source/destination aren't taking into account the absolute file path being specified for App.xaml:
<GeneratedXamlSrc0 Condition="'%(AllProjectXamlPages.Link)'==''" Include="@(AllProjectXamlPages->'$(XamlGeneratedOutputPath)%(Identity)')" />
App.xaml has its file path specified differently because it is a solution-level item ("$(MSBuildThisFileDirectory)App.xaml").
The easiest way to solve this problem is to specify a link attribute for the App.xaml file inside the HubApp.Shared.projitems build target file, in the HubApp.Shared directory. This will override the faulty logic and specify a relative path that works correctly with the XAML copying build step. Inside the .projitems file you'll find the following code:
<ApplicationDefinition Include="$(MSBuildThisFileDirectory)App.xaml">
<SubType>Designer</SubType>
</ApplicationDefinition>
Replace this with:
<ApplicationDefinition Include="$(MSBuildThisFileDirectory)App.xaml">
<SubType>Designer</SubType>
<Link>App.xaml</Link>
</ApplicationDefinition>
.. Then reset the NCrunch engine. The projects should now build correctly.
I've also raised this issue with MS, as I'm sure they won't want it in the RTM -
https://connect.microsoft.com/VisualStudio/feedback/details/856162/build-problem-in-template-hub-app-universal-apps#