12GB of ram is not enough for 2 GPU's and GPU acceleration. You really need more ram for that. I would also suggest increasing the ram besides cc_merchant's comments on the Disk setup. I would try setting the Nvidia control panel to just use 1 GPU for acceleration and select the primary. Then see if the performance changes much. Even though both GPU's are not used for playback just enabling the 2nd will still lock down ram for the 2nd GPU.
Eric
ADK