We have an application that uses PrismV2. It is multitargeted using the project linker. It's split into about 5 modules. 4 are shared on both silverlight and desktop and one is specifically built for the desktop version.
The project builds perfectly in the IDE but Team Foundation Build fails to build to project. I think it builds it but it fails to copy the assemblies correctly to the drop location and fails the build.
I can't think of any way to fix this aside from splitting the application into seperate solution files. How has your team solved this problem? I'm assuming you are using some kind of CI.