Please try to install MSI Afterburner or GPU-Z and monitor your clock frequency. It's possible that one GPU is running at a lower clock frequency.
12.3 worked as in now they are both giving around 550 each, which is around stock.
Now I am using CGminer and it doesn't seem to implement my gpu changes like lowering the memory clock, lowering the voltage or changing the core clock. I have 12.3 install and no afterburner. What would cause this? Do I need to modify the config file instead of doing through the command line?
7970 and cgminer don't mix well. Use Afterburner to change memory and voltages. When in cgminer, voltage is always stuck; however, it is not really that value. Use GPU-z or afterburner to see the actual voltage. Memory likes to "stick" in afterburner, so I set memory in afterburner, then set it to the same in cgminer.
Also: Close youtube. Turn off hardware acceleration with flash (rightclick on a youtube video -> settings -> uncheck enable hardware acceleration) Hardware acceleration sticks the card in 2D mode with 500mhz clock.