My old herding instructor told me once that she hated working with dogs who came to herding with a ton of obedience training because it was difficult to train some of the conditioned responses out.
Tanner was pretty good about remaining focused on the sheep, but even he would turn and look at me when he heard the down command (it was kind of cute, really, almost like he was shocked that I would tell him to down because didn't I know there were FREAKING SHEEP RIGHT OVER THERE!!!).
What helped me was to stop using his name before the command. That helped decrease the head turning and loss of focus a lot. Also, I practiced it a lot away from the sheep, during off leash exercise out in the open range or in my back yard. The more common it was the easier it was for Tanner to handle.
It does get better!