Please tell us more about this card, Is it a flashed (for Mac) card? AGP or PCI? I have had cards that one DVI port went out on and the second port works.
I really do not like the idea of partitioned drives with two systems. I prefer having that second system on a second drive. If for nothing else using one drive to check the other. I have also had issues with monitor drivers on machines with newer clean installs of 10.8 +.