In the Configure Options in TV you can set the order in which the tuners will be used if more than one tuner is available.
I have two tuners and put Hauppauge WinTV PVR2 USB2 at the top. But MC doesn't preserve this order. When I leave Configuration and go back to it again the Hauppauge WinTV PVR PCI II is at the top again (see attached picture).