When turning one of the 2D-Renderwindows into a 3D Renderwindow, both 3D Windows start glitching. Looks like a camera placement problem.
These two lines of code are sufficient ro reproduce the problem:
mitk::BaseRenderer* renderer = mitk::BaseRenderer::GetInstance(this->GetRenderWindowPart()->GetRenderWindow("sagittal")->GetRenderWindow());
renderer->SetMapperID(mitk::BaseRenderer::Standard3D);
Markus had a look at it already. Seems like this condition currently prevents displaying two 3D Renderwindows at the same time.