If you have the console on top and move your mouse over the MITK main window it comes on top automatically. This is very confusing.
This behaviour is caused by the code
#ifdef Q_OS_MAC
this->show(); this->setWindowOpacity(0.0f);
#else
this->setVisible(false);
#endif
in file QmitkRenderWindowMenu.cpp.
It may work when using the Mac OS code also for windows.