It sounds to me like there might be a config file hiding somewhere that is keeping the second card in "2D" mode.
Uninstall the video drivers, CCC and Trixx. Reboot into safe mode and Run Driver Sweeper to get rid of any ATI left overs.
http://www.guru3d.com/category/driversweeper/
After that, re-install your drivers and hopefully you'll be good to go.