Unfortunately, I cannot find any benchmarks for blu-ray encoding using the exact same resolution as the blu-ray movie itself. I recommend you do a test; encode a blu-ray movie down to 720p (1280x720) resolution and compare your frame rates to the following:
If you get similar results then there is nothing wrong with your system. As mentioned before, the higher the resolution, the slower the encoding time. Encoding using the x.264 codec is pretty slow especially during the 2nd pass. It's the price you must pay if you want the high quality that the x.264 codec can output.