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It is Visual Studio (msbuild/vcbuild/devenv) that actually performs the building of a VS solution or project, not VBP itself. Building a VS project from the command-line is not identical to building in the VS IDE. If building via MSBuild does not work, you might try using devenv (enter devenv in the Override field on the Advanced tab), as this will be closer to what the IDE does when building. You can check the 'Display the compiler command-line' checkbox on the Advanced tab and rebuild the step, to determine the command-line being used and reproduce outside VBP (and provide to MS when submitting a support incident).
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