SOLVED
Turns out since I was running one DVI and one HDMI the second DVI slot couldn't be DVI-VGA. I purchased a straight through DVI dual link cable and presto 3 monitors. Windows was fine with the DVI to VGA on one DVI port and one DVI to HDMI on the second DVI but OS X was not, it's a driver issue in OS X that hopefully 10.8.3 has fixed.
To anyone reading this and wondering if it is fixable, good news it is as simple as ensuring the two monitors on the DVI ports are DVI-D cables, you can use DVI-D to HDMI or whatever you like but it has to be DVI-D.
The mistake I made was running one DVI port at DVI-D and one at DVI-I.
Two DVI-D is required if using both the DVI ports in OS X, at least with the latest drivers available in OS X and from Nvidia.
Really simple mistake to make and hopefully this helps someone. Thank you for everyones input.