Even when built from VBP, it's still VS/MSBuild that actually scans dependencies and determines what needs to be built for a VS project/solution. Building via
devenv rather than MSBuild might help, but even that is not necessarily identical to building in the IDE.
If that doesn't resolve the problem, you would need to contact MS support regarding the issue. You can check the 'Display compiler command-line' checkbox on the Options tab, rebuild, and copy the command-line used to reproduce outside VBP and provide with your support material.