Thanks Nino, I've worked out what the problem is and it's all my dodgy techs fault (that's me in case anyone's wondering ;0) ) I forgot that I'd also adjusted the top out hole kicker because whenever it kicked a ball out it would hit the first of the two little metal posts under the large ball gate (pic below) and bounce back in the hole again. Anyway I've disturbed the normally open button switch in the hole so that it was sitting there closed all the time. Thus the reason that both the targets would stay up and the second ball would launch out. As far as the game could tell there was already a ball in the out hole.
Thanks for the tips though and you are dead right about the new targets. I had to adjust them acouple of times before I had them working correctly. This last one, the x3 was a particularly stubborn one.