are you using gpu tweak to oc the cards? there is a "locked" mode. when you oc one card, it will sync with the 2nd card and apply the same settings. otherwise you have to oc the cards individually by selecting card 1 and card 2, applying both settings.
There is a lock logo between core clock and core voltage on the left side. when 2 cards are detected you should see a drop down menu to switch between card 1 and 2
Well, I'm going to say the tool is bugged. It will not let me OC 2 cards. Only one. It detects the card I can choose in the monitor panel but not in the main panel. I can use Afterburner with no problem. Sucks.
Figured it out. You have to put your cursor over the box to the right of the 3D box and then a pop up appears and you can do it then. That should be changed or at least put something there to indicate this.