Manual Focus distance in movie render queue

I have only just started using the Movie Render Queue and I found that the outputted images are out of focus. It seems the manual Focus distance set in the sequencer is different in the output from the movie render queue. I am finding that I have to increase this number by about 30-40% in the sequencer in order to attain the focus distance that I need in the output. Am I missing something here? I am using the 16:9 DSLR camera.