why send it back to MVVS when it runs good? It is the setup in your model that is causing the problem, not the engine itself.
Engines often do run different when in the model. You have to tune the needles again, due to vibrations and/or changes in carb membrane reference pressure.
Header the same? Same length? If it runs hotter in the model, your header needs to be longer to compensate. Add about two inches to the header length and start from there.