It looks to me like your rail protector on the right rail is causing your trouble. the manual shooter rod fires the ball further back and from a single point on the ball. So when it hits the ball it may jeck to the right and catch the edge of the rail protector sending it left into the drain lane. The automatic shooter contacts the ball in two places and flings it forward nice and straight.
I'd move the protector back. I can take a picture of how mine is installed but I'll have to wait till I get home from work.
Brian