The constructor of QmlMitkRenderWindowItem uses the standard name "QML Render Window" for all instances. Since this name is also used for the renderer you cannot use renderer specific properties anymore.
Here is the constructor:
QmlMitkRenderWindowItem(QQuickItem* parent = 0, const QString& name = "QML render window", mitk::VtkPropRenderer* renderer = NULL, mitk::RenderingManager* renderingManager = NULL)
mitk::RenderWindowBase::Initialize(renderingManager, name); GetInstances()[QVTKQuickItem::GetRenderWindow()] = this;