I were facing the same problem like yours, even I am using a new update of Encoder.
I tried to export directly via Premiere CS6, and I got an amazing result. PPCS6 exports faster than Encoder CS6 does. While PPCS6 was working, I used GPU monitor to see what happening. Very surprised, the percentage of using GPU (CUDA) when PPCS6 was exporting was very high (from 27 to 80 percent load), and CPU was being used about 50 percent. This is opposite to the case of using Encoder exporting. It is usually using about 6-12 percent of GPU resource.